diff --git a/CHANGES.rst b/CHANGES.rst
index 2b1a782015..c92f63ffc5 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -4,7 +4,10 @@
 New Features
 ------------
 
-* New design for viewer legend. [#3220, #3254, #3263]
+-  New design for viewer legend. [#3220, #3254, #3263]
+
+- Helper classes (Imviz, Specviz, etc) now have ``reset_app`` method to reset the
+  application to a fresh state. [#3273]
 
 Cubeviz
 ^^^^^^^
@@ -74,7 +77,7 @@ Bug Fixes
 - Fixed Aperture Photometry radial profile fit crashing when NaN is present in
   aperture data for Cubeviz and Imviz. [#3246]
 
-- Prevent PluginMarks from converting y-range so they maintain their position 
+- Prevent PluginMarks from converting y-range so they maintain their position
   in the spectrum-viewer when spectral y units are converted. [#3242]
 
 Cubeviz
diff --git a/jdaviz/app.py b/jdaviz/app.py
index bcc0c405b2..7bd1c6a8b7 100644
--- a/jdaviz/app.py
+++ b/jdaviz/app.py
@@ -571,6 +571,7 @@ def _on_layers_changed(self, msg):
             children_layers = self._get_assoc_data_children(layer_name)
 
         elif hasattr(msg, 'subset'):
+            print("Got subset message")
             layer_name = msg.subset.label
             is_wcs_only = False
             is_not_child = True
@@ -1723,6 +1724,7 @@ def get_viewer_ids(self, prefix=None):
     def get_viewer_reference_names(self):
         """Return a list of available viewer reference names."""
         # Cannot sort because of None
+
         return [self._viewer_item_by_id(vid).get('reference') for vid in self._viewer_store]
 
     def _update_viewer_reference_name(
@@ -2769,8 +2771,15 @@ def compose_viewer_area(viewer_area_items):
     def _reset_state(self):
         """ Resets the application state """
         self.state = ApplicationState()
+        self._viewer_store = {}
         self._application_handler._tools = {}
 
+        # Need to re-add callbacks to emit messages when icons are updated
+        self.state.add_callback('viewer_icons',
+                                lambda value: self.hub.broadcast(IconsUpdatedMessage('viewer', value, sender=self)))  # noqa
+        self.state.add_callback('layer_icons',
+                                lambda value: self.hub.broadcast(IconsUpdatedMessage('layer', value, sender=self)))  # noqa
+
     def get_configuration(self, path=None, section=None):
         """Returns a copy of the application configuration.
 
diff --git a/jdaviz/core/helpers.py b/jdaviz/core/helpers.py
index ebee7d0e86..14621840d6 100644
--- a/jdaviz/core/helpers.py
+++ b/jdaviz/core/helpers.py
@@ -464,6 +464,27 @@ def show_in_new_tab(self, title=None):  # pragma: no cover
                       DeprecationWarning)
         return self.show(loc="sidecar:tab-after", title=title)
 
+    def reset_app(self):
+        """
+        Re-initialize the entire application. Any current settings and loaded data will
+        be lost.
+        """
+        # Remove all data from the data collection
+        data = [d for d in self.app.data_collection]
+        for d in data:
+            self.app.data_collection.remove(d)
+
+        # Remove all subsets from the data collection
+        subsets = [s for s in self.app.data_collection.subset_groups]
+        for s in subsets:
+            self.app.data_collection.remove_subset_group(s)
+
+        # Remove existing subsets from the edit subset menu
+        self.app.session.edit_subset_mode.edit_subset = []
+
+        # Reset everything else
+        self.app.load_configuration(self.app._loaded_configuration)
+
     def _handle_display_units(self, data, use_display_units=True):
         if use_display_units:
             if isinstance(data, Spectrum1D):