diff --git a/mokelumne/util/file_transfer.py b/mokelumne/util/file_transfer.py
index d8b4f5b..e26604c 100644
--- a/mokelumne/util/file_transfer.py
+++ b/mokelumne/util/file_transfer.py
@@ -20,19 +20,34 @@ def sha256_for_file(path: Path) -> str:
     return sha256.hexdigest()
 
 
+def _should_include_manifest_entry(relative_path: Path, item: Path) -> bool:
+    """Return True when a path should be added to the manifest."""
+    if any(part.startswith(".") for part in relative_path.parts):
+        return False
+
+    if item.name.casefold() in {"thumbs.db"}:
+        return False
+
+    return True
+
 def build_file_manifest(source_path: Path) -> Manifest:
     files = []
 
     for item in source_path.rglob("*"):
-        if item.is_file():
-            relative_path = item.relative_to(source_path)
-            files.append(
-                {
-                    "path": str(relative_path),
-                    "size": item.stat().st_size,
-                    "sha256": sha256_for_file(item),
-                }
-            )
+        if not item.is_file():
+            continue
+
+        relative_path = item.relative_to(source_path)
+        if not _should_include_manifest_entry(relative_path, item):
+            continue
+
+        files.append(
+            {
+                "path": str(relative_path),
+                "size": item.stat().st_size,
+                "sha256": sha256_for_file(item),
+            }
+        )
     
     return {
         "source_root": str(source_path),
diff --git a/test/unit/test_file_transfer.py b/test/unit/test_file_transfer.py
index dd6b40b..53be53c 100644
--- a/test/unit/test_file_transfer.py
+++ b/test/unit/test_file_transfer.py
@@ -69,6 +69,32 @@ def test_build_manifest_includes_nested_files(self, tmp_path: Path):
         }
         assert len(result) == 2
 
+    def test_build_manifest_excludes_hidden_and_excluded_files(self, tmp_path: Path):
+        """Ensure that build_manifest skips hidden and system junk files."""
+        visible_file = tmp_path / "visible.tif"
+        visible_file.write_text("hello", encoding="utf-8")
+
+        hidden_file = tmp_path / ".hidden.txt"
+        hidden_file.write_text("secret", encoding="utf-8")
+
+        hidden_dir = tmp_path / ".hidden"
+        hidden_dir.mkdir()
+        hidden_dir_file = hidden_dir / "nested.txt"
+        hidden_dir_file.write_text("nested", encoding="utf-8")
+
+        ds_store = tmp_path / ".DS_Store"
+        ds_store.write_text("folder metadata", encoding="utf-8")
+
+        thumbs_db = tmp_path / "Thumbs.db"
+        thumbs_db.write_text("thumbnail images db", encoding="utf-8")
+
+        result = file_transfer.build_file_manifest(tmp_path)
+
+        paths = {entry["path"] for entry in result["files"]}
+
+        assert paths == {"visible.tif"}
+        assert len(result["files"]) == 1
+
     def test_verify_manifest_success(self, tmp_path: Path):
         """Ensure verify_manifest succeeds for valid files."""