diff --git a/thicket/ensemble.py b/thicket/ensemble.py
index c129175a..1535c501 100644
--- a/thicket/ensemble.py
+++ b/thicket/ensemble.py
@@ -76,21 +76,21 @@ def _check_structures():
             """Check that the structures of the thicket objects are valid for the incoming operations."""
             # Required/expected format of the data
             for th in thickets:
-                verify_thicket_structures(th.dataframe, index=["node", "profile"])
+                assert th.dataframe.index.nlevels == 2
+                assert th.metadata.index.nlevels == 1
+                assert th.dataframe.index.names[1] == th.metadata.index.name
                 verify_thicket_structures(th.statsframe.dataframe, index=["node"])
-                verify_thicket_structures(th.metadata, index=["profile"])
             # Check for metadata_key in metadata
             if metadata_key:
                 for th in thickets:
-                    verify_thicket_structures(th.metadata, columns=[metadata_key])
+                    if metadata_key != th.metadata.index.name:
+                        verify_thicket_structures(th.metadata, columns=[metadata_key])
             # Check length of profiles match if metadata key is not provided
             if metadata_key is None:
                 for i in range(len(thickets) - 1):
                     if len(thickets[i].profile) != len(thickets[i + 1].profile):
                         raise ValueError(
-                            "Length of all thicket profiles must match if 'metadata_key' is not provided. {} != {}".format(
-                                len(thickets[i].profile), len(thickets[i + 1].profile)
-                            )
+                            f"Length of all thicket profiles must match if 'metadata_key' is not provided. {len(thickets[i].profile)} != {len(thickets[i + 1].profile)}"
                         )
             # Ensure all thickets profiles are sorted. Must be true when metadata_key=None to
             # guarantee performance data table and metadata table match up.
@@ -120,14 +120,16 @@ def _create_multiindex_columns(df, upper_idx_name):
         def _handle_metadata():
             """Handle operations to create new concatenated columnar axis metadata table."""
             # Update index to reflect performance data table index
-            for i in range(len(thickets_cp)):
-                thickets_cp[i].metadata.reset_index(drop=True, inplace=True)
+            if metadata_key != inner_idx:
+                for i in range(len(thickets_cp)):
+                    thickets_cp[i].metadata.reset_index(drop=True, inplace=True)
             if metadata_key is None:
                 for i in range(len(thickets_cp)):
                     thickets_cp[i].metadata.index.set_names("profile", inplace=True)
             else:
                 for i in range(len(thickets_cp)):
-                    thickets_cp[i].metadata.set_index(metadata_key, inplace=True)
+                    if metadata_key != inner_idx:
+                        thickets_cp[i].metadata.set_index(metadata_key, inplace=True)
                     thickets_cp[i].metadata.sort_index(inplace=True)
 
             # Create multi-index columns
@@ -179,17 +181,17 @@ def _handle_perfdata():
                     thickets_cp[i].metadata_column_to_perfdata(
                         "new_profiles", drop=True
                     )
-                    thickets_cp[i].dataframe.reset_index(level="profile", inplace=True)
+                    thickets_cp[i].dataframe.reset_index(level=inner_idx, inplace=True)
                     new_mappings.update(
                         pd.Series(
                             thickets_cp[i]
                             .dataframe["new_profiles"]
                             .map(lambda x: (x, headers[i]))
                             .values,
-                            index=thickets_cp[i].dataframe["profile"],
+                            index=thickets_cp[i].dataframe[inner_idx],
                         ).to_dict()
                     )
-                    thickets_cp[i].dataframe.drop("profile", axis=1, inplace=True)
+                    thickets_cp[i].dataframe.drop(inner_idx, axis=1, inplace=True)
                     thickets_cp[i].dataframe.set_index(
                         "new_profiles", append=True, inplace=True
                     )
@@ -198,18 +200,20 @@ def _handle_perfdata():
                     )
             else:  # Change second-level index to be from metadata's "metadata_key" column
                 for i in range(len(thickets_cp)):
-                    thickets_cp[i].metadata_column_to_perfdata(metadata_key)
-                    thickets_cp[i].dataframe.reset_index(level="profile", inplace=True)
+                    if metadata_key not in thickets_cp[i].dataframe.index.names:
+                        thickets_cp[i].metadata_column_to_perfdata(metadata_key)
+                    thickets_cp[i].dataframe.reset_index(level=inner_idx, inplace=True)
                     new_mappings.update(
                         pd.Series(
                             thickets_cp[i]
                             .dataframe[metadata_key]
                             .map(lambda x: (x, headers[i]))
                             .values,
-                            index=thickets_cp[i].dataframe["profile"],
+                            index=thickets_cp[i].dataframe[inner_idx],
                         ).to_dict()
                     )
-                    thickets_cp[i].dataframe.drop("profile", axis=1, inplace=True)
+                    if inner_idx != metadata_key:
+                        thickets_cp[i].dataframe.drop(inner_idx, axis=1, inplace=True)
                     thickets_cp[i].dataframe.set_index(
                         metadata_key, append=True, inplace=True
                     )
@@ -266,11 +270,12 @@ def _handle_statsframe():
                 ),
             )
 
-        # Step 0A: Pre-check of data structures
-        _check_structures()
-        # Step 0B: Variable Initialization
+        # Step 0A: Variable Initialization
         combined_th = thickets[0].deepcopy()
         thickets_cp = [th.deepcopy() for th in thickets]
+        inner_idx = thickets_cp[0].dataframe.index.names[1]
+        # Step 0B: Pre-check of data structures
+        _check_structures()
 
         # Step 1: Unify the thickets
         union_graph, _thickets = Ensemble._unify(thickets_cp)
diff --git a/thicket/utils.py b/thicket/utils.py
index 3f2c2435..0fd09239 100644
--- a/thicket/utils.py
+++ b/thicket/utils.py
@@ -55,7 +55,11 @@ def verify_sorted_profile(thicket_component):
         thicket_component (DataFrame): component of thicket to check
     """
     profile_index_values = list(
-        OrderedDict.fromkeys(thicket_component.index.get_level_values("profile"))
+        OrderedDict.fromkeys(
+            thicket_component.index.get_level_values(
+                thicket_component.index.nlevels - 1
+            )  # Innermost index
+        )
     )
     if profile_index_values != sorted(profile_index_values):
         raise ValueError(