diff --git a/src/twinkle/template/base.py b/src/twinkle/template/base.py
index acc17d2e..b33ad449 100644
--- a/src/twinkle/template/base.py
+++ b/src/twinkle/template/base.py
@@ -362,25 +362,30 @@ def _is_trajectory(self, obj: Any) -> bool:
         """Check if an object is a Trajectory (has 'messages' key)."""
         return isinstance(obj, Mapping) and 'messages' in obj
 
-    def _get_trajectory_keys(self, columnar: Mapping) -> List[str]:
-        """Get keys whose values are lists of Trajectories in columnar format."""
+    def _get_trajectory_keys(self, trajectories: Mapping, is_columnar: bool) -> List[str]:
+        """Get keys whose values are lists of Trajectories."""
         keys = []
-        for k, v in columnar.items():
-            if isinstance(v, list) and v and self._is_trajectory(v[0]):
-                keys.append(k)
+        if is_columnar:
+            for k, v in trajectories.items():
+                if isinstance(v, list) and v and self._is_trajectory(v[0]):
+                    keys.append(k)
+        else:
+            for k, v in trajectories.items():
+                if v and self._is_trajectory(v):
+                    keys.append(k)
         return keys
 
     def batch_encode(
         self,
-        trajectories: Union[Dict[str, Any], List[Trajectory]],
+        trajectories: Union[Dict[str, List[Any]], List[Trajectory]],
         add_generation_prompt: bool = False,
     ) -> Union[Dict[str, Any], List[InputFeature]]:
         """Encode trajectories into InputFeatures.
 
         Args:
             trajectories: Either List[Trajectory] or columnar Dict[str, List].
-                For DPO, columnar format with 'positive'/'negative' keys containing
-                List[Trajectory] is supported.
+                For nested trajectories, columnar format with trajectory list columns
+                (e.g., 'chosen'/'rejected') is supported.
             add_generation_prompt: Whether to add generation prompt.
 
         Returns:
@@ -388,21 +393,27 @@ def batch_encode(
         """
         _transfer = False
 
+        # Handle list input
+        if isinstance(trajectories, list) and len(trajectories) > 0:
+            # Check if first element has nested trajectories
+            if isinstance(trajectories[0], Mapping) and len(self._get_trajectory_keys(trajectories[0], False)) > 0:
+                # Convert row→columnar, process with columnar logic, convert back
+                columnar = self.map_row_to_col(trajectories)
+                encoded = self.batch_encode(columnar, add_generation_prompt)
+                return self.map_col_to_row(encoded)
+
         if isinstance(trajectories, Mapping):
             _transfer = True
-            # Check if it has trajectory list columns (DPO format)
-            traj_keys = self._get_trajectory_keys(trajectories)
+            # Check if it has nested trajectory columns
+            traj_keys = self._get_trajectory_keys(trajectories, True)
             if traj_keys:
-                # DPO format: encode each trajectory list separately, keep other columns
-                result = {}
-                for key in trajectories:
-                    if key in traj_keys:
-                        # Encode this trajectory list
-                        result[key] = self.batch_encode(trajectories[key], add_generation_prompt=add_generation_prompt)
-                    else:
-                        # Keep non-trajectory columns as-is
-                        result[key] = trajectories[key]
-                return result
+                # Nested format: encode each trajectory list separately, keep other columns
+                return {
+                    key:
+                    self.batch_encode(trajectories[key], add_generation_prompt)
+                    if key in traj_keys else trajectories[key]
+                    for key in trajectories
+                }
             else:
                 # Standard columnar format
                 trajectories = self.map_col_to_row(trajectories)