diff --git a/NEWS.md b/NEWS.md
index 0f1c08079c9..f3dbe84cb39 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,6 +3,7 @@
 * Added support for setting custom properties on the project (#2903)
 * Removed Space and Ctrl+Space shortcuts from Layers view to avoid conflict with panning (#3672)
 * Scripting: Added API for editing tile layers using terrain sets (with a-morphous, #3758)
+* Scripting: Support erasing tiles in Tool.preview and TileMap.merge
 * Fixed object preview position with parallax factor on group layer (#3669)
 * Fixed hover highlight rendering with active parallax factor (#3669)
 * Fixed updating of object selection outlines when changing parallax factor (#3669)
diff --git a/src/libtiled/map.cpp b/src/libtiled/map.cpp
index f9f84f03542..45fc178d613 100644
--- a/src/libtiled/map.cpp
+++ b/src/libtiled/map.cpp
@@ -518,12 +518,12 @@ QRect Map::tileBoundingRect() const
     return mapBounds;
 }
 
-QRegion Map::tileRegion() const
+QRegion Map::modifiedTileRegion() const
 {
     QRegion region;
     LayerIterator it(this, Layer::TileLayerType);
     while (auto tileLayer = static_cast<TileLayer*>(it.next()))
-        region |= tileLayer->region();
+        region |= tileLayer->modifiedRegion();
     return region;
 }
 
diff --git a/src/libtiled/map.h b/src/libtiled/map.h
index 36bf7293453..0abee3233e7 100644
--- a/src/libtiled/map.h
+++ b/src/libtiled/map.h
@@ -314,7 +314,7 @@ class TILEDSHARED_EXPORT Map : public Object
     MapObject *findObjectById(int objectId) const;
 
     QRect tileBoundingRect() const;
-    QRegion tileRegion() const;
+    QRegion modifiedTileRegion() const;
 
 private:
     friend class GroupLayer;    // so it can call adoptLayer
diff --git a/src/libtiled/tilelayer.h b/src/libtiled/tilelayer.h
index cda636ec09d..5607e76affb 100644
--- a/src/libtiled/tilelayer.h
+++ b/src/libtiled/tilelayer.h
@@ -380,6 +380,7 @@ class TILEDSHARED_EXPORT TileLayer : public Layer
 
     QRegion region(std::function<bool (const Cell &)> condition) const;
     QRegion region() const;
+    QRegion modifiedRegion() const;
 
     const Cell &cellAt(int x, int y) const;
     const Cell &cellAt(QPoint point) const;
@@ -626,6 +627,17 @@ inline QRegion TileLayer::region() const
     return region([] (const Cell &cell) { return !cell.isEmpty(); });
 }
 
+/**
+ * Calculates the modified region of this layer. This includes both all
+ * non-empty cells as well as any cells that were marked as "checked".
+ */
+inline QRegion TileLayer::modifiedRegion() const
+{
+    return region([] (const Cell &cell) {
+        return !cell.isEmpty() || cell.checked();
+    });
+}
+
 /**
  * Returns a read-only reference to the cell at the given coordinates. The
  * coordinates have to be within this layer.
diff --git a/src/tiled/brushitem.cpp b/src/tiled/brushitem.cpp
index 1139548e64f..23056b6d31e 100644
--- a/src/tiled/brushitem.cpp
+++ b/src/tiled/brushitem.cpp
@@ -73,11 +73,8 @@ void BrushItem::clear()
  */
 void BrushItem::setTileLayer(const SharedTileLayer &tileLayer)
 {
-    mTileLayer = tileLayer;
-    mRegion = tileLayer ? tileLayer->region() : QRegion();
-
-    updateBoundingRect();
-    update();
+    setTileLayer(tileLayer,
+                 tileLayer ? tileLayer->modifiedRegion() : QRegion());
 }
 
 /**
@@ -97,11 +94,7 @@ void BrushItem::setTileLayer(const SharedTileLayer &tileLayer,
 
 void BrushItem::setMap(const SharedMap &map)
 {
-    mMap = map;
-    mRegion = map->tileRegion();
-
-    updateBoundingRect();
-    update();
+    setMap(map, map->modifiedTileRegion());
 }
 
 void BrushItem::setMap(const SharedMap &map, const QRegion &region)
diff --git a/src/tiled/brushitem.h b/src/tiled/brushitem.h
index 30a88eabf35..8c313cad2f0 100644
--- a/src/tiled/brushitem.h
+++ b/src/tiled/brushitem.h
@@ -65,7 +65,7 @@ class BrushItem : public QGraphicsItem
                QWidget *widget = nullptr) override;
 
 protected:
-    MapDocument *mapDocument() const  { return mMapDocument; }
+    MapDocument *mapDocument() const { return mMapDocument; }
 
 private:
     void updateBoundingRect();
diff --git a/src/tiled/capturestamphelper.cpp b/src/tiled/capturestamphelper.cpp
index 3ece4979d15..be6b21d6d83 100644
--- a/src/tiled/capturestamphelper.cpp
+++ b/src/tiled/capturestamphelper.cpp
@@ -22,7 +22,6 @@
 
 #include "map.h"
 #include "mapdocument.h"
-#include "tilelayer.h"
 
 #include <memory>
 
diff --git a/src/tiled/mapdocument.cpp b/src/tiled/mapdocument.cpp
index 49455e9a70d..d8bb893f7a0 100644
--- a/src/tiled/mapdocument.cpp
+++ b/src/tiled/mapdocument.cpp
@@ -992,8 +992,8 @@ void MapDocument::paintTileLayers(const Map &map, bool mergeable,
         auto source = sourceLayers[i];
         auto target = targetLayers[i];
 
-        const QRegion editedRegion = source->region();
-        if (editedRegion.isEmpty())
+        const QRegion paintRegion = source->modifiedRegion();
+        if (paintRegion.isEmpty())
             continue;
 
         std::unique_ptr<TileLayer> newLayer;
@@ -1018,7 +1018,7 @@ void MapDocument::paintTileLayers(const Map &map, bool mergeable,
                                                           source->x(),
                                                           source->y(),
                                                           source,
-                                                          editedRegion);
+                                                          paintRegion);
 
         if (missingTilesets && !missingTilesets->isEmpty()) {
             for (const SharedTileset &tileset : std::as_const(*missingTilesets)) {
@@ -1058,7 +1058,7 @@ void MapDocument::paintTileLayers(const Map &map, bool mergeable,
         paintCommand->setMergeable(mergeable);
         undoStack()->push(paintCommand);
 
-        regions[target] |= editedRegion;
+        regions[target] |= paintRegion;
 
         mergeable = true; // further paints are always mergeable
     }
diff --git a/src/tiled/stampbrush.cpp b/src/tiled/stampbrush.cpp
index 89cce23b68b..70660d51542 100644
--- a/src/tiled/stampbrush.cpp
+++ b/src/tiled/stampbrush.cpp
@@ -529,7 +529,7 @@ void StampBrush::drawPreviewLayer(const QVector<QPoint> &points)
             if (regionCache.contains(map)) {
                 stampRegion = regionCache.value(map);
             } else {
-                stampRegion = map->tileRegion();
+                stampRegion = map->modifiedTileRegion();
                 regionCache.insert(map, stampRegion);
             }
 
@@ -635,7 +635,7 @@ void StampBrush::updatePreview(QPoint tilePos)
         }
 
         if (mPreviewMap)
-            tileRegion = mPreviewMap->tileRegion();
+            tileRegion = mPreviewMap->modifiedTileRegion();
 
         if (tileRegion.isEmpty())
             tileRegion = QRect(tilePos, tilePos);