diff --git a/frontend/src/core/tools/Merge.tsx b/frontend/src/core/tools/Merge.tsx
index e725291db..05d358f70 100644
--- a/frontend/src/core/tools/Merge.tsx
+++ b/frontend/src/core/tools/Merge.tsx
@@ -26,6 +26,57 @@ const Merge = (props: BaseToolProps) => {
     props,
     { minFiles: 2 }
   );
+  const naturalCompare = useCallback((a: string, b: string): number => {
+    const isDigit = (char: string) => char >= '0' && char <= '9';
+
+    const getChunk = (s: string, length: number, marker: number): { chunk: string; newMarker: number } => {
+      let chunk = '';
+      const c = s.charAt(marker);
+      chunk += c;
+      marker++;
+
+      if (isDigit(c)) {
+        while (marker < length && isDigit(s.charAt(marker))) {
+          chunk += s.charAt(marker);
+          marker++;
+        }
+      } else {
+        while (marker < length && !isDigit(s.charAt(marker))) {
+          chunk += s.charAt(marker);
+          marker++;
+        }
+      }
+      return { chunk, newMarker: marker };
+    };
+
+    const len1 = a.length;
+    const len2 = b.length;
+    let marker1 = 0;
+    let marker2 = 0;
+
+    while (marker1 < len1 && marker2 < len2) {
+      const { chunk: chunk1, newMarker: newMarker1 } = getChunk(a, len1, marker1);
+      marker1 = newMarker1;
+
+      const { chunk: chunk2, newMarker: newMarker2 } = getChunk(b, len2, marker2);
+      marker2 = newMarker2;
+
+      let result: number;
+      if (isDigit(chunk1.charAt(0)) && isDigit(chunk2.charAt(0))) {
+        const num1 = parseInt(chunk1, 10);
+        const num2 = parseInt(chunk2, 10);
+        result = num1 - num2;
+      } else {
+        result = chunk1.localeCompare(chunk2);
+      }
+
+      if (result !== 0) {
+        return result;
+      }
+    }
+
+    return len1 - len2;
+  }, []);
 
   // Custom file sorting logic for merge tool
   const sortFiles = useCallback((sortType: 'filename' | 'dateModified', ascending: boolean = true) => {
@@ -33,7 +84,7 @@ const Merge = (props: BaseToolProps) => {
       let comparison = 0;
       switch (sortType) {
         case 'filename':
-          comparison = stubA.name.localeCompare(stubB.name);
+          comparison = naturalCompare(stubA.name, stubB.name);
           break;
         case 'dateModified':
           comparison = stubA.lastModified - stubB.lastModified;
@@ -45,7 +96,7 @@ const Merge = (props: BaseToolProps) => {
     const selectedIds = sortedStubs.map(record => record.id);
     const deselectedIds = fileIds.filter(id => !selectedIds.includes(id));
     reorderFiles([...selectedIds, ...deselectedIds]);
-  }, [selectedFileStubs, fileIds, reorderFiles]);
+  }, [selectedFileStubs, fileIds, reorderFiles, naturalCompare]);
 
   return createToolFlow({
     files: {