diff --git a/gpx/src/gpx.ts b/gpx/src/gpx.ts
index 39662e5c..cc32e928 100644
--- a/gpx/src/gpx.ts
+++ b/gpx/src/gpx.ts
@@ -274,6 +274,42 @@ export class GPXFile extends GPXTreeNode<Track>{
             draft.trk = freeze(trk); // Pre-freeze the array, faster as well
         });
     }
+
+    clean(bounds: [Coordinates, Coordinates], inside: boolean, deleteTrackPoints: boolean, deleteWaypoints: boolean, trackIndices?: number[], segmentIndices?: number[], waypointIndices?: number[]) {
+        return produce(this, (draft) => {
+            let og = getOriginal(draft); // Read as much as possible from the original object because it is faster
+            if (deleteTrackPoints) {
+                let trk = og.trk.slice();
+                let i = 0;
+                let trackIndex = 0;
+                while (i < trk.length) {
+                    if (trackIndices === undefined || trackIndices.includes(trackIndex)) {
+                        trk[i] = trk[i].clean(bounds, inside, segmentIndices);
+                        if (trk[i].getNumberOfTrackPoints() === 0) {
+                            trk.splice(i, 1);
+                        } else {
+                            i++;
+                        }
+                    } else {
+                        i++;
+                    }
+                    trackIndex++;
+                }
+                draft.trk = freeze(trk); // Pre-freeze the array, faster as well
+            }
+            if (deleteWaypoints) {
+                let wpt = og.wpt.filter((point, waypointIndex) => {
+                    if (waypointIndices === undefined || waypointIndices.includes(waypointIndex)) {
+                        let inBounds = point.attributes.lat >= bounds[0].lat && point.attributes.lat <= bounds[1].lat && point.attributes.lon >= bounds[0].lon && point.attributes.lon <= bounds[1].lon;
+                        return inBounds !== inside;
+                    } else {
+                        return true;
+                    }
+                });
+                draft.wpt = freeze(wpt); // Pre-freeze the array, faster as well
+            }
+        });
+    }
 };
 
 // A class that represents a Track in a GPX file
@@ -414,6 +450,29 @@ export class Track extends GPXTreeNode<TrackSegment> {
             draft.trkseg = freeze(trkseg); // Pre-freeze the array, faster as well
         });
     }
+
+    clean(bounds: [Coordinates, Coordinates], inside: boolean, segmentIndices?: number[]) {
+        return produce(this, (draft) => {
+            let og = getOriginal(draft); // Read as much as possible from the original object because it is faster
+            let trkseg = og.trkseg.slice();
+            let i = 0;
+            let segmentIndex = 0;
+            while (i < trkseg.length) {
+                if (segmentIndices === undefined || segmentIndices.includes(segmentIndex)) {
+                    trkseg[i] = trkseg[i].clean(bounds, inside);
+                    if (trkseg[i].getNumberOfTrackPoints() === 0) {
+                        trkseg.splice(i, 1);
+                    } else {
+                        i++;
+                    }
+                } else {
+                    i++;
+                }
+                segmentIndex++;
+            }
+            draft.trkseg = freeze(trkseg); // Pre-freeze the array, faster as well
+        });
+    }
 };
 
 // A class that represents a TrackSegment in a GPX file
@@ -616,6 +675,17 @@ export class TrackSegment extends GPXTreeLeaf {
             draft.trkpt = freeze(trkpt); // Pre-freeze the array, faster as well
         });
     }
+
+    clean(bounds: [Coordinates, Coordinates], inside: boolean) {
+        return produce(this, (draft) => {
+            let og = getOriginal(draft); // Read as much as possible from the original object because it is faster
+            let trkpt = og.trkpt.filter((point) => {
+                let inBounds = point.attributes.lat >= bounds[0].lat && point.attributes.lat <= bounds[1].lat && point.attributes.lon >= bounds[0].lon && point.attributes.lon <= bounds[1].lon;
+                return inBounds !== inside;
+            });
+            draft.trkpt = freeze(trkpt); // Pre-freeze the array, faster as well
+        });
+    }
 };
 
 export class TrackPoint {
diff --git a/website/src/lib/components/toolbar/Toolbar.svelte b/website/src/lib/components/toolbar/Toolbar.svelte
index 49584eb5..51bf8512 100644
--- a/website/src/lib/components/toolbar/Toolbar.svelte
+++ b/website/src/lib/components/toolbar/Toolbar.svelte
@@ -52,7 +52,7 @@
 			</ToolbarItem>
 			<ToolbarItem tool={Tool.CLEAN}>
 				<SquareDashedMousePointer slot="icon" size="18" />
-				<span slot="tooltip">{$_('toolbar.clean_tooltip')}</span>
+				<span slot="tooltip">{$_('toolbar.clean.tooltip')}</span>
 			</ToolbarItem>
 			<ToolbarItem tool={Tool.STYLE}>
 				<Palette slot="icon" size="18" />
diff --git a/website/src/lib/components/toolbar/ToolbarItemMenu.svelte b/website/src/lib/components/toolbar/ToolbarItemMenu.svelte
index d3b8a8c1..4dd34230 100644
--- a/website/src/lib/components/toolbar/ToolbarItemMenu.svelte
+++ b/website/src/lib/components/toolbar/ToolbarItemMenu.svelte
@@ -6,6 +6,7 @@
 	import Scissors from '$lib/components/toolbar/tools/Scissors.svelte';
 	import Waypoint from '$lib/components/toolbar/tools/Waypoint.svelte';
 	import Merge from '$lib/components/toolbar/tools/Merge.svelte';
+	import Clean from '$lib/components/toolbar/tools/Clean.svelte';
 	import RoutingControlPopup from '$lib/components/toolbar/tools/routing/RoutingControlPopup.svelte';
 	import { onMount } from 'svelte';
 	import mapboxgl from 'mapbox-gl';
@@ -39,6 +40,8 @@
 						<Waypoint />
 					{:else if $currentTool === Tool.MERGE}
 						<Merge />
+					{:else if $currentTool === Tool.CLEAN}
+						<Clean />
 					{/if}
 				</Card.Content>
 			</Card.Root>
diff --git a/website/src/lib/components/toolbar/tools/Clean.svelte b/website/src/lib/components/toolbar/tools/Clean.svelte
new file mode 100644
index 00000000..a3c0f6a7
--- /dev/null
+++ b/website/src/lib/components/toolbar/tools/Clean.svelte
@@ -0,0 +1,177 @@
+<script lang="ts" context="module">
+	enum CleanType {
+		INSIDE = 'inside',
+		OUTSIDE = 'outside'
+	}
+</script>
+
+<script lang="ts">
+	import { Label } from '$lib/components/ui/label/index.js';
+	import { Checkbox } from '$lib/components/ui/checkbox';
+	import * as RadioGroup from '$lib/components/ui/radio-group';
+	import { Button } from '$lib/components/ui/button';
+	import Help from '$lib/components/Help.svelte';
+	import { _ } from 'svelte-i18n';
+	import { onDestroy, onMount } from 'svelte';
+	import { resetCursor, setCrosshairCursor } from '$lib/utils';
+	import { Trash2 } from 'lucide-svelte';
+	import { map } from '$lib/stores';
+	import { selection } from '$lib/components/file-list/Selection';
+	import { dbUtils } from '$lib/db';
+
+	let cleanType = CleanType.INSIDE;
+	let deleteTrackpoints = true;
+	let deleteWaypoints = true;
+	let rectangleCoordinates: mapboxgl.LngLat[] = [];
+
+	function updateRectangle() {
+		if ($map) {
+			if (rectangleCoordinates.length != 2) {
+				if ($map.getLayer('rectangle')) {
+					$map.removeLayer('rectangle');
+				}
+			} else {
+				let data = {
+					type: 'Feature',
+					geometry: {
+						type: 'Polygon',
+						coordinates: [
+							[
+								[rectangleCoordinates[0].lng, rectangleCoordinates[0].lat],
+								[rectangleCoordinates[1].lng, rectangleCoordinates[0].lat],
+								[rectangleCoordinates[1].lng, rectangleCoordinates[1].lat],
+								[rectangleCoordinates[0].lng, rectangleCoordinates[1].lat],
+								[rectangleCoordinates[0].lng, rectangleCoordinates[0].lat]
+							]
+						]
+					}
+				};
+				let source = $map.getSource('rectangle');
+				if (source) {
+					source.setData(data);
+				} else {
+					$map.addSource('rectangle', {
+						type: 'geojson',
+						data: data
+					});
+				}
+				if (!$map.getLayer('rectangle')) {
+					$map.addLayer({
+						id: 'rectangle',
+						type: 'fill',
+						source: 'rectangle',
+						paint: {
+							'fill-color': 'SteelBlue',
+							'fill-opacity': 0.5
+						}
+					});
+				}
+			}
+		}
+	}
+
+	$: if (rectangleCoordinates) {
+		updateRectangle();
+	}
+
+	let mousedown = false;
+	function onMouseDown(e: any) {
+		mousedown = true;
+		rectangleCoordinates = [e.lngLat, e.lngLat];
+	}
+
+	function onMouseMove(e: any) {
+		if (mousedown) {
+			rectangleCoordinates[1] = e.lngLat;
+		}
+	}
+
+	function onMouseUp(e: any) {
+		mousedown = false;
+	}
+
+	onMount(() => {
+		setCrosshairCursor();
+	});
+
+	$: if ($map) {
+		$map.on('mousedown', onMouseDown);
+		$map.on('mousemove', onMouseMove);
+		$map.on('mouseup', onMouseUp);
+		$map.dragPan.disable();
+	}
+
+	onDestroy(() => {
+		resetCursor();
+		if ($map) {
+			$map.off('mousedown', onMouseDown);
+			$map.off('mousemove', onMouseMove);
+			$map.off('mouseup', onMouseUp);
+			$map.dragPan.enable();
+
+			if ($map.getLayer('rectangle')) {
+				$map.removeLayer('rectangle');
+			}
+			if ($map.getSource('rectangle')) {
+				$map.removeSource('rectangle');
+			}
+		}
+	});
+
+	$: validSelection = $selection.size > 0;
+</script>
+
+<div class="flex flex-col gap-3 max-w-80">
+	<fieldset class="flex flex-col gap-3">
+		<Label class="flex flex-row items-center gap-[6.4px] h-3">
+			<Checkbox bind:checked={deleteTrackpoints} class="scale-90" />
+			{$_('toolbar.clean.delete_trackpoints')}
+		</Label>
+		<Label class="flex flex-row items-center gap-[6.4px] h-3">
+			<Checkbox bind:checked={deleteWaypoints} class="scale-90" />
+			{$_('toolbar.clean.delete_waypoints')}
+		</Label>
+		<RadioGroup.Root bind:value={cleanType}>
+			<Label class="flex flex-row items-center gap-2">
+				<RadioGroup.Item value={CleanType.INSIDE} />
+				{$_('toolbar.clean.delete_inside')}
+			</Label>
+			<Label class="flex flex-row items-center gap-2">
+				<RadioGroup.Item value={CleanType.OUTSIDE} />
+				{$_('toolbar.clean.delete_outside')}
+			</Label>
+		</RadioGroup.Root>
+	</fieldset>
+	<Button
+		variant="outline"
+		disabled={!validSelection || rectangleCoordinates.length != 2}
+		on:click={() => {
+			dbUtils.cleanSelection(
+				[
+					{
+						lat: Math.min(rectangleCoordinates[0].lat, rectangleCoordinates[1].lat),
+						lon: Math.min(rectangleCoordinates[0].lng, rectangleCoordinates[1].lng)
+					},
+					{
+						lat: Math.max(rectangleCoordinates[0].lat, rectangleCoordinates[1].lat),
+						lon: Math.max(rectangleCoordinates[0].lng, rectangleCoordinates[1].lng)
+					}
+				],
+				cleanType === CleanType.INSIDE,
+				deleteTrackpoints,
+				deleteWaypoints
+			);
+			rectangleCoordinates = [];
+		}}
+	>
+		<Trash2 size="16" class="mr-1" />
+		{$_('toolbar.clean.button')}
+	</Button>
+	<Help>
+		{#if validSelection}
+			{$_('toolbar.clean.help')}
+		{:else}
+			{$_('toolbar.clean.help_no_selection')}
+		{/if}
+	</Help>
+</div>
diff --git a/website/src/lib/db.ts b/website/src/lib/db.ts
index cbc6db33..83c82fc9 100644
--- a/website/src/lib/db.ts
+++ b/website/src/lib/db.ts
@@ -647,6 +647,35 @@ export const dbUtils = {
             }
         });
     },
+    cleanSelection: (bounds: [Coordinates, Coordinates], inside: boolean, deleteTrackPoints: boolean, deleteWaypoints: boolean) => {
+        if (get(selection).size === 0) {
+            return;
+        }
+        applyGlobal((draft) => {
+            applyToOrderedSelectedItemsFromFile((fileId, level, items) => {
+                let file = original(draft)?.get(fileId);
+                if (file) {
+                    let newFile = file;
+                    if (level === ListLevel.FILE) {
+                        newFile = file.clean(bounds, inside, deleteTrackPoints, deleteWaypoints);
+                    } else if (level === ListLevel.TRACK) {
+                        let trackIndices = items.map((item) => (item as ListTrackItem).getTrackIndex());
+                        newFile = newFile.clean(bounds, inside, deleteTrackPoints, false, trackIndices);
+                    } else if (level === ListLevel.SEGMENT) {
+                        let trackIndices = [(items[0] as ListTrackSegmentItem).getTrackIndex()];
+                        let segmentIndices = items.map((item) => (item as ListTrackSegmentItem).getSegmentIndex());
+                        newFile = newFile.clean(bounds, inside, deleteTrackPoints, false, trackIndices, segmentIndices);
+                    } else if (level === ListLevel.WAYPOINTS) {
+                        newFile = newFile.clean(bounds, inside, false, deleteWaypoints);
+                    } else if (level === ListLevel.WAYPOINT) {
+                        let waypointIndices = items.map((item) => (item as ListWaypointItem).getWaypointIndex());
+                        newFile = newFile.clean(bounds, inside, false, deleteWaypoints, [], [], waypointIndices);
+                    }
+                    draft.set(newFile._data.id, freeze(newFile));
+                }
+            });
+        });
+    },
     deleteSelection: () => {
         if (get(selection).size === 0) {
             return;
diff --git a/website/src/locales/en.json b/website/src/locales/en.json
index 5e07aaeb..b58387ec 100644
--- a/website/src/locales/en.json
+++ b/website/src/locales/en.json
@@ -131,7 +131,16 @@
         "extract_tooltip": "Extract inner tracks or segments",
         "waypoint_tooltip": "Create and edit points of interest",
         "reduce_tooltip": "Reduce the number of GPS points",
-        "clean_tooltip": "Clean GPS points and points of interest with a rectangle selection",
+        "clean": {
+            "tooltip": "Clean GPS points and points of interest with a rectangle selection",
+            "delete_trackpoints": "Delete GPS points",
+            "delete_waypoints": "Delete points of interest",
+            "delete_inside": "Delete inside selection",
+            "delete_outside": "Delete outside selection",
+            "button": "Delete",
+            "help": "Select a rectangle area on the map to remove GPS points and points of interest",
+            "help_no_selection": "Select a file element to use the tool"
+        },
         "style_tooltip": "Change the style of the trace"
     },
     "layers": {