diff --git a/apps/emqx_ft/src/emqx_ft_storage_fs.erl b/apps/emqx_ft/src/emqx_ft_storage_fs.erl
index e2bda8fcb..cc9d94b35 100644
--- a/apps/emqx_ft/src/emqx_ft_storage_fs.erl
+++ b/apps/emqx_ft/src/emqx_ft_storage_fs.erl
@@ -49,9 +49,11 @@
 
 -type filefrag() :: filefrag({filemeta, filemeta()} | {segment, segmentinfo()}).
 
+-define(FRAGDIR, frags).
+-define(TEMPDIR, tmp).
+-define(RESULTDIR, result).
 -define(MANIFEST, "MANIFEST.json").
 -define(SEGMENT, "SEG").
--define(TEMP, "TMP").
 
 -type root() :: file:name().
 
@@ -77,7 +79,7 @@
     % Quota? Some lower level errors?
     {ok, emqx_ft_storage:ctx()} | {error, conflict} | {error, _TODO}.
 store_filemeta(Storage, Transfer, Meta) ->
-    Filepath = mk_filepath(Storage, Transfer, ?MANIFEST),
+    Filepath = mk_filepath(Storage, Transfer, [?FRAGDIR], ?MANIFEST),
     case read_file(Filepath, fun decode_filemeta/1) of
         {ok, Meta} ->
             _ = touch_file(Filepath),
@@ -89,7 +91,7 @@ store_filemeta(Storage, Transfer, Meta) ->
             % about it too much now.
             {error, conflict};
         {error, Reason} when Reason =:= notfound; Reason =:= corrupted; Reason =:= enoent ->
-            write_file_atomic(Filepath, encode_filemeta(Meta))
+            write_file_atomic(Storage, Transfer, Filepath, encode_filemeta(Meta))
     end.
 
 %% Store a segment in the backing filesystem.
@@ -99,15 +101,15 @@ store_filemeta(Storage, Transfer, Meta) ->
     % Quota? Some lower level errors?
     ok | {error, _TODO}.
 store_segment(Storage, Transfer, Segment = {_Offset, Content}) ->
-    Filepath = mk_filepath(Storage, Transfer, mk_segment_filename(Segment)),
-    write_file_atomic(Filepath, Content).
+    Filepath = mk_filepath(Storage, Transfer, [?FRAGDIR], mk_segment_filename(Segment)),
+    write_file_atomic(Storage, Transfer, Filepath, Content).
 
 -spec list(storage(), transfer()) ->
     % Some lower level errors? {error, notfound}?
     % Result will contain zero or only one filemeta.
     {ok, list(filefrag())} | {error, _TODO}.
 list(Storage, Transfer) ->
-    Dirname = mk_filedir(Storage, Transfer),
+    Dirname = mk_filedir(Storage, Transfer, [?FRAGDIR]),
     case file:list_dir(Dirname) of
         {ok, Filenames} ->
             {ok, filtermap_files(fun mk_filefrag/2, Dirname, Filenames)};
@@ -151,8 +153,8 @@ assemble(Storage, Transfer, Callback) ->
     {ok, handle()} | {error, _TODO}.
 open_file(Storage, Transfer, Filemeta) ->
     Filename = maps:get(name, Filemeta),
-    Filepath = mk_filepath(Storage, Transfer, Filename),
-    TempFilepath = mk_temp_filepath(Filepath),
+    TempFilepath = mk_temp_filepath(Storage, Transfer, Filename),
+    _ = filelib:ensure_dir(TempFilepath),
     case file:open(TempFilepath, [write, raw]) of
         {ok, Handle} ->
             _ = file:truncate(Handle),
@@ -174,11 +176,11 @@ write({Filepath, IoDevice, Ctx}, IoData) ->
 -spec complete(storage(), transfer(), filemeta(), handle()) ->
     ok | {error, {checksum, _Algo, _Computed}} | {error, _TODO}.
 complete(Storage, Transfer, Filemeta, Handle = {Filepath, IoDevice, Ctx}) ->
-    TargetFilepath = mk_filepath(Storage, Transfer, maps:get(name, Filemeta)),
+    TargetFilepath = mk_filepath(Storage, Transfer, [?RESULTDIR], maps:get(name, Filemeta)),
     case verify_checksum(Ctx, Filemeta) of
         ok ->
             ok = file:close(IoDevice),
-            file:rename(Filepath, TargetFilepath);
+            mv_temp_file(Filepath, TargetFilepath);
         {error, _} = Error ->
             _ = discard(Handle),
             Error
@@ -284,11 +286,11 @@ break_segment_filename(Filename) ->
             {error, invalid}
     end.
 
-mk_filedir(Storage, {ClientId, FileId}) ->
-    filename:join([get_storage_root(Storage), ClientId, FileId]).
+mk_filedir(Storage, {ClientId, FileId}, SubDirs) ->
+    filename:join([get_storage_root(Storage), ClientId, FileId | SubDirs]).
 
-mk_filepath(Storage, Transfer, Filename) ->
-    filename:join(mk_filedir(Storage, Transfer), Filename).
+mk_filepath(Storage, Transfer, SubDirs, Filename) ->
+    filename:join(mk_filedir(Storage, Transfer, SubDirs), Filename).
 
 get_storage_root(Storage) ->
     maps:get(root, Storage, filename:join(emqx:data_dir(), "file_transfer")).
@@ -315,13 +317,13 @@ safe_decode(Content, DecodeFun) ->
             {error, corrupted}
     end.
 
-write_file_atomic(Filepath, Content) when is_binary(Content) ->
-    TempFilepath = mk_temp_filepath(Filepath),
+write_file_atomic(Storage, Transfer, Filepath, Content) when is_binary(Content) ->
+    TempFilepath = mk_temp_filepath(Storage, Transfer, filename:basename(Filepath)),
     Result = emqx_misc:pipeline(
         [
             fun filelib:ensure_dir/1,
             fun write_contents/2,
-            fun(FP) -> mv_temp_file(Filepath, FP) end
+            fun(_) -> mv_temp_file(TempFilepath, Filepath) end
         ],
         TempFilepath,
         Content
@@ -334,11 +336,9 @@ write_file_atomic(Filepath, Content) when is_binary(Content) ->
             {error, Reason}
     end.
 
-mk_temp_filepath(Filepath) ->
-    Dirname = filename:dirname(Filepath),
-    Filename = filename:basename(Filepath),
+mk_temp_filepath(Storage, Transfer, Filename) ->
     Unique = erlang:unique_integer([positive]),
-    filename:join(Dirname, mk_filename([?TEMP, Unique, ".", Filename])).
+    filename:join(mk_filedir(Storage, Transfer, [?TEMPDIR]), mk_filename([Unique, ".", Filename])).
 
 mk_filename(Comps) ->
     lists:append(lists:map(fun mk_filename_component/1, Comps)).
@@ -351,7 +351,8 @@ mk_filename_component(S) when is_list(S) -> S.
 write_contents(Filepath, Content) ->
     file:write_file(Filepath, Content).
 
-mv_temp_file(Filepath, TempFilepath) ->
+mv_temp_file(TempFilepath, Filepath) ->
+    _ = filelib:ensure_dir(Filepath),
     file:rename(TempFilepath, Filepath).
 
 touch_file(Filepath) ->
@@ -365,7 +366,8 @@ mk_filefrag(Dirname, Filename = ?MANIFEST) ->
     mk_filefrag(Dirname, Filename, filemeta, fun read_filemeta/2);
 mk_filefrag(Dirname, Filename = ?SEGMENT ++ _) ->
     mk_filefrag(Dirname, Filename, segment, fun read_segmentinfo/2);
-mk_filefrag(_Dirname, _) ->
+mk_filefrag(_Dirname, _Filename) ->
+    % TODO this is unexpected, worth logging?
     false.
 
 mk_filefrag(Dirname, Filename, Tag, Fun) ->
@@ -380,6 +382,7 @@ mk_filefrag(Dirname, Filename, Tag, Fun) ->
                 fragment => {Tag, Frag}
             }};
         {error, _Reason} ->
+            % TODO loss of information
             false
     end.
 
diff --git a/apps/emqx_ft/test/emqx_ft_assembler_SUITE.erl b/apps/emqx_ft/test/emqx_ft_assembler_SUITE.erl
index 9ec2fce61..fdfdd432e 100644
--- a/apps/emqx_ft/test/emqx_ft_assembler_SUITE.erl
+++ b/apps/emqx_ft/test/emqx_ft_assembler_SUITE.erl
@@ -133,7 +133,7 @@ t_assemble_complete_local_transfer(Config) ->
     ).
 
 mk_assembly_filename(Config, {ClientID, FileID}, Filename) ->
-    filename:join([?config(storage_root, Config), ClientID, FileID, Filename]).
+    filename:join([?config(storage_root, Config), ClientID, FileID, result, Filename]).
 
 on_assembly_finished(Result) ->
     ?tp(test_assembly_finished, #{result => Result}).