diff --git a/cmd/dotmesh-server/s3.go b/cmd/dotmesh-server/s3.go
index 4e0eafe35..9544e590b 100644
--- a/cmd/dotmesh-server/s3.go
+++ b/cmd/dotmesh-server/s3.go
@@ -232,9 +232,25 @@ func downloadS3Object(downloader *s3manager.Downloader, key, versionId, bucket,
 	return nil
 }
 
-func removeOldS3Files(keyToVersionIds map[string]string, paths map[string]int64, bucket string, svc *s3.S3) (map[string]string, error) {
+func removeOldS3Files(keyToVersionIds map[string]string, paths map[string]int64, bucket string, prefixes []string, svc *s3.S3) (map[string]string, error) {
+	if len(prefixes) == 0 {
+		return removeOldPrefixedS3Files(keyToVersionIds, paths, bucket, "", svc)
+	}
+	var err error
+	for _, prefix := range prefixes {
+		keyToVersionIds, err = removeOldPrefixedS3Files(keyToVersionIds, paths, bucket, prefix, svc)
+		if err != nil {
+			return nil, err
+		}
+	}
+	return keyToVersionIds, nil
+}
+func removeOldPrefixedS3Files(keyToVersionIds map[string]string, paths map[string]int64, bucket, prefix string, svc *s3.S3) (map[string]string, error) {
 	// get a list of the objects in s3, if there's anything there that isn't in our list of files in dotmesh, delete it.
 	params := &s3.ListObjectsV2Input{Bucket: aws.String(bucket)}
+	if prefix != "" {
+		params.SetPrefix(prefix)
+	}
 	var innerError error
 	err := svc.ListObjectsV2Pages(params, func(output *s3.ListObjectsV2Output, lastPage bool) bool {
 		for _, item := range output.Contents {
@@ -260,10 +276,19 @@ func removeOldS3Files(keyToVersionIds map[string]string, paths map[string]int64,
 	return keyToVersionIds, nil
 }
 
-func updateS3Files(keyToVersionIds map[string]string, paths map[string]int64, pathToMount, transferRequestId, bucket string, svc *s3.S3, pollResult TransferPollResult) (map[string]string, error) {
+func updateS3Files(keyToVersionIds map[string]string, paths map[string]int64, pathToMount, transferRequestId, bucket string, prefixes []string, svc *s3.S3, pollResult TransferPollResult) (map[string]string, error) {
 	// push every key up to s3 and then send back a map of object key -> s3 version id
 	uploader := s3manager.NewUploaderWithClient(svc)
-	for key, size := range paths {
+	// filter out any paths we don't care about in an S3 remote
+	filtered := make(map[string]int64)
+	for _, elem := range prefixes {
+		for key, size := range paths {
+			if strings.HasPrefix(key, elem) {
+				filtered[key] = size
+			}
+		}
+	}
+	for key, size := range filtered {
 		path := fmt.Sprintf("%s/%s", pathToMount, key)
 		file, err := os.Open(path)
 		pollResult.Index += 1
diff --git a/cmd/dotmesh-server/s3pushinitiatorstate.go b/cmd/dotmesh-server/s3pushinitiatorstate.go
index 025133ad6..fd1e77d3a 100644
--- a/cmd/dotmesh-server/s3pushinitiatorstate.go
+++ b/cmd/dotmesh-server/s3pushinitiatorstate.go
@@ -73,12 +73,12 @@ func s3PushInitiatorState(f *fsMachine) stateFn {
 			return backoffState
 		}
 		keyToVersionIds := make(map[string]string)
-		keyToVersionIds, err = updateS3Files(keyToVersionIds, paths, pathToMount, transferRequestId, transferRequest.RemoteName, svc, pollResult)
+		keyToVersionIds, err = updateS3Files(keyToVersionIds, paths, pathToMount, transferRequestId, transferRequest.RemoteName, transferRequest.Prefixes, svc, pollResult)
 		if err != nil {
 			f.errorDuringTransfer("error-updating-s3-objects", err)
 			return backoffState
 		}
-		keyToVersionIds, err = removeOldS3Files(keyToVersionIds, paths, transferRequest.RemoteName, svc)
+		keyToVersionIds, err = removeOldS3Files(keyToVersionIds, paths, transferRequest.RemoteName, transferRequest.Prefixes, svc)
 		if err != nil {
 			f.errorDuringTransfer("error-during-object-pagination", err)
 			return backoffState
diff --git a/tests/s3_test.go b/tests/s3_test.go
index 74be949e7..b48b8a5eb 100644
--- a/tests/s3_test.go
+++ b/tests/s3_test.go
@@ -220,22 +220,31 @@ func TestS3Remote(t *testing.T) {
 		}
 	})
 
-	t.Run("CloneSubsetPull", func(t *testing.T) {
-		// fsname := citools.UniqName()
-		// citools.RunOnNode(t, node1, "dm s3 clone-subset test-real-s3 test.dotmesh subset/ --local-name="+fsname)
-		// citools.RunOnNode(t, node1, "dm push test-real-s3 "+fsname)
-		// resp := citools.OutputFromRunOnNode(t, node1, s3cmd+" ls s3://test.dotmesh")
-		// if !strings.Contains(resp, "hello-world.txt") {
-		// 	citools.RunOnNode(t, node1, s3cmd+" put hello-world.txt s3://test.dotmesh")
-		// 	t.Error("Deleted a file we aren't tracking")
-		// }
+	t.Run("CloneSubsetPushPull", func(t *testing.T) {
+		fsname := citools.UniqName()
+		citools.RunOnNode(t, node1, "dm s3 clone-subset test-real-s3 test.dotmesh subset/ --local-name="+fsname)
+		citools.RunOnNode(t, node1, citools.DockerRun(fsname)+" touch /foo/file.txt")
+		citools.TryUntilSucceeds(func() error {
+			output := citools.OutputFromRunOnNode(t, node1, "dm dot show "+fsname+" -H | grep dirty")
+			if strings.Contains(output, "\t0") {
+				return fmt.Errorf("not dirty yet")
+			}
+			return nil
+		}, "waiting for dirty data...")
+		citools.RunOnNode(t, node1, "dm commit -m 'add file to s3'")
+		citools.RunOnNode(t, node1, "dm push test-real-s3 "+fsname)
+		resp := citools.OutputFromRunOnNode(t, node1, s3cmd("ls s3://test.dotmesh"))
+		if !strings.Contains(resp, "hello-world.txt") {
+			citools.RunOnNode(t, node1, s3cmd("put hello-world.txt s3://test.dotmesh"))
+			t.Error("Deleted a file we aren't tracking")
+		}
 		PutBackS3Files(node1)
 		citools.RunOnNode(t, node1, "mkdir -p subset && echo 'directories' > subset/subdir.txt")
 		citools.RunOnNode(t, node1, s3cmd("put subset/subdir.txt s3://test.dotmesh/subset/subdir.txt"))
 		fsname2 := citools.UniqName()
 		citools.RunOnNode(t, node1, "dm s3 clone-subset test-real-s3 test.dotmesh subset/ --local-name="+fsname2)
 		citools.RunOnNode(t, node1, "dm pull test-real-s3 "+fsname2)
-		resp := citools.OutputFromRunOnNode(t, node1, citools.DockerRun(fsname2)+" ls /foo/")
+		resp = citools.OutputFromRunOnNode(t, node1, citools.DockerRun(fsname2)+" ls /foo/")
 		if strings.Contains(resp, "hello-world.txt") {
 			t.Error("Pulled down a file we aren't tracking")
 		}