diff --git a/src/libslic3r/ExPolygon.cpp b/src/libslic3r/ExPolygon.cpp
index 489023041..506ba8cb6 100644
--- a/src/libslic3r/ExPolygon.cpp
+++ b/src/libslic3r/ExPolygon.cpp
@@ -372,6 +372,27 @@ bool remove_sticks(ExPolygon &poly)
     return remove_sticks(poly.contour) || remove_sticks(poly.holes);
 }
 
+bool remove_small_and_small_holes(ExPolygons &expolygons, double min_area)
+{
+    bool   modified = false;
+    size_t free_idx = 0;
+    for (size_t expoly_idx = 0; expoly_idx < expolygons.size(); ++expoly_idx) {
+        if (std::abs(expolygons[expoly_idx].area()) >= min_area) {
+            // Expolygon is big enough, so also check all its holes
+            modified |= remove_small(expolygons[expoly_idx].holes, min_area);
+            if (free_idx < expoly_idx) {
+                std::swap(expolygons[expoly_idx].contour, expolygons[free_idx].contour);
+                std::swap(expolygons[expoly_idx].holes, expolygons[free_idx].holes);
+            }
+            ++free_idx;
+        } else
+            modified = true;
+    }
+    if (free_idx < expolygons.size())
+        expolygons.erase(expolygons.begin() + free_idx, expolygons.end());
+    return modified;
+}
+
 void keep_largest_contour_only(ExPolygons &polygons)
 {
 	if (polygons.size() > 1) {
diff --git a/src/libslic3r/ExPolygon.hpp b/src/libslic3r/ExPolygon.hpp
index 73770bb18..89ba2e006 100644
--- a/src/libslic3r/ExPolygon.hpp
+++ b/src/libslic3r/ExPolygon.hpp
@@ -360,6 +360,9 @@ extern std::vector<BoundingBox> get_extents_vector(const ExPolygons &polygons);
 extern bool        remove_sticks(ExPolygon &poly);
 extern void 	   keep_largest_contour_only(ExPolygons &polygons);
 
+// Removes all expolygons smaller than min_area and also removes all holes smaller than min_area
+extern bool        remove_small_and_small_holes(ExPolygons &expolygons, double min_area);
+
 inline double area(const ExPolygons &polys)
 {
     double s = 0.;
diff --git a/src/libslic3r/MultiMaterialSegmentation.cpp b/src/libslic3r/MultiMaterialSegmentation.cpp
index aa2536108..1ed08ef4b 100644
--- a/src/libslic3r/MultiMaterialSegmentation.cpp
+++ b/src/libslic3r/MultiMaterialSegmentation.cpp
@@ -1357,13 +1357,27 @@ std::vector<std::vector<std::pair<ExPolygon, size_t>>> multi_material_segmentati
     std::vector<std::vector<PaintedLine>>                  painted_lines(print_object.layers().size());
     std::vector<EdgeGrid::Grid>                            edge_grids(print_object.layers().size());
     const ConstLayerPtrsAdaptor                            layers = print_object.layers();
+    std::vector<Polygons>                                  input_polygons(layers.size());
+
+    // Merge all regions and remove small holes
+    for(size_t layer_idx = 0; layer_idx < layers.size(); layer_idx += 1) {
+        ExPolygons ex_polygons;
+        for (LayerRegion *region : layers[layer_idx]->regions())
+            for (const Surface &surface : region->slices.surfaces)
+                Slic3r::append(ex_polygons, offset_ex(surface.expolygon, SCALED_EPSILON));
+        // All expolygons are expanded by SCALED_EPSILON, merged, and then shrunk again by SCALED_EPSILON
+        // to ensure that very close polygons will be merged.
+        ex_polygons = union_ex(ex_polygons);
+        // Remove all expolygons and holes with an area less than 0.01mm^2
+        remove_small_and_small_holes(ex_polygons, Slic3r::sqr(scale_(0.1f)));
+        input_polygons[layer_idx] = to_polygons(union_ex(offset_ex(ex_polygons, -SCALED_EPSILON)));
+    }
 
     for (size_t layer_idx = 0; layer_idx < layers.size(); ++layer_idx) {
-        const Layer *layer = layers[layer_idx];
-        BoundingBox  bbox(get_extents(layer->lslices));
+        BoundingBox  bbox(get_extents(input_polygons[layer_idx]));
         bbox.offset(SCALED_EPSILON);
         edge_grids[layer_idx].set_bbox(bbox);
-        edge_grids[layer_idx].create(layer->lslices, coord_t(scale_(10.)));
+        edge_grids[layer_idx].create(input_polygons[layer_idx], coord_t(scale_(10.)));
     }
 
     for (const ModelVolume *mv : print_object.model_object()->volumes) {
@@ -1453,11 +1467,7 @@ std::vector<std::vector<std::pair<ExPolygon, size_t>>> multi_material_segmentati
             std::vector<PaintedLine> &painted_lines_single = painted_lines[layer_idx];
 
             if (!painted_lines_single.empty()) {
-                Polygons original_polygons;
-                for (const Slic3r::EdgeGrid::Contour &contour : edge_grids[layer_idx].contours())
-                    original_polygons.emplace_back(Points(contour.begin(), contour.end()));
-
-                std::vector<std::vector<ColoredLine>> color_poly = colorize_polygons(original_polygons, painted_lines_single);
+                std::vector<std::vector<ColoredLine>> color_poly = colorize_polygons(input_polygons[layer_idx], painted_lines_single);
                 MMU_Graph                             graph      = build_graph(layer_idx, color_poly);
                 remove_multiple_edges_in_vertices(graph, color_poly);
                 graph.remove_nodes_with_one_arc();
diff --git a/src/libslic3r/PrintObject.cpp b/src/libslic3r/PrintObject.cpp
index 1c5c4f021..688b7d360 100644
--- a/src/libslic3r/PrintObject.cpp
+++ b/src/libslic3r/PrintObject.cpp
@@ -1906,15 +1906,6 @@ void PrintObject::_slice(const std::vector<coordf_t> &layer_height_profile)
 
     // --------------------MMU_SEGMENTATION_BEGIN----------------------
 
-    // Temporary fix for not assigned lslices
-    for(size_t layer_idx = 0; layer_idx < m_layers.size(); layer_idx += 1) {
-        ExPolygons ex_polygons;
-        for (LayerRegion *region : this->m_layers[layer_idx]->regions())
-            for (const Surface &surface : region->slices.surfaces)
-                ex_polygons.emplace_back(surface.expolygon);
-        this->m_layers[layer_idx]->lslices = union_ex(ex_polygons);
-    }
-
     size_t region_count_before_change = this->num_regions();
     std::vector<std::vector<std::pair<ExPolygon, size_t>>> segmented_regions = multi_material_segmentation_by_painting(*this);
     // Skip region with default extruder