diff --git a/plugins/extensions/pykrita/plugin/plugins/filtermanager/components/filtermanagertreemodel.py b/plugins/extensions/pykrita/plugin/plugins/filtermanager/components/filtermanagertreemodel.py
--- a/plugins/extensions/pykrita/plugin/plugins/filtermanager/components/filtermanagertreemodel.py
+++ b/plugins/extensions/pykrita/plugin/plugins/filtermanager/components/filtermanagertreemodel.py
@@ -6,6 +6,7 @@
 
 class FilterManagerTreeModel(QAbstractItemModel):
 
+    TYPE_COLUMN = 1
     NODE_COLUMN = 3
     DOCUMENT_COLUMN = 4
 
@@ -72,6 +73,9 @@
         if role == Qt.UserRole + 2:
             return item.data(self.DOCUMENT_COLUMN)
 
+        if role == Qt.UserRole + 3:
+            return item.data(self.TYPE_COLUMN)
+
         if role != Qt.DisplayRole and role != Qt.DecorationRole:
             return None
 
diff --git a/plugins/extensions/pykrita/plugin/plugins/filtermanager/uifiltermanager.py b/plugins/extensions/pykrita/plugin/plugins/filtermanager/uifiltermanager.py
--- a/plugins/extensions/pykrita/plugin/plugins/filtermanager/uifiltermanager.py
+++ b/plugins/extensions/pykrita/plugin/plugins/filtermanager/uifiltermanager.py
@@ -26,7 +26,7 @@
         self.buttonBox.accepted.connect(self.confirmButton)
         self.buttonBox.rejected.connect(self.mainDialog.close)
 
-        self.documentsTreeView.setSelectionMode(QAbstractItemView.MultiSelection)
+        self.documentsTreeView.setSelectionMode(QAbstractItemView.SingleSelection)
         self.mainDialog.setWindowModality(Qt.NonModal)
 
     def initialize(self):
@@ -54,16 +54,39 @@
         self.mainDialog.activateWindow()
 
     def confirmButton(self):
+        documentsIndexes = []
+
         selectionModel = self.documentsTreeView.selectionModel()
         for index in selectionModel.selectedRows():
             node = self.treeModel.data(index, Qt.UserRole + 1)
             documentIndex = self.treeModel.data(index, Qt.UserRole + 2)
-            self.applyFilterOverNode(node, self.documents[documentIndex])
+            _type = self.treeModel.data(index, Qt.UserRole + 3)
+
+            if _type == 'Document':
+                self.applyFilterOverDocument(self.documents[documentIndex])
+            else:
+                self.applyFilterOverNode(node, self.documents[documentIndex])
+
+            documentsIndexes.append(documentIndex)
+
+        self.refreshDocumentsProjections(set(documentsIndexes))
+
+    def refreshDocumentsProjections(self, indexes):
+        for index in indexes:
+            document = self.documents[index]
+            document.refreshProjection()
 
     def applyFilterOverNode(self, node, document):
         _filter = self.kritaInstance.filter(self.filterComboBox.currentText())
         _filter.apply(node, 0, 0, document.width(), document.height())
 
+    def applyFilterOverDocument(self, document):
+        """ This method applies the selected filter just to topLevelNodes, then
+            if topLevelNodes are GroupLayers, that filter will not be applied. """
+
+        for node in document.topLevelNodes():
+            self.applyFilterOverNode(node, document)
+
     @property
     def filters(self):
         return self._filters