diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryController.java b/laboratory/src/org/labkey/laboratory/LaboratoryController.java
index 31dedddc..0f85b4fe 100644
--- a/laboratory/src/org/labkey/laboratory/LaboratoryController.java
+++ b/laboratory/src/org/labkey/laboratory/LaboratoryController.java
@@ -89,6 +89,7 @@
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.laboratory.assay.AssayHelper;
 import org.labkey.laboratory.query.WorkbookModel;
+import org.labkey.vfs.FileLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -620,8 +621,8 @@ protected File getTargetFile(String filename) throws IOException
 
             try
             {
-                File targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
-                return AssayFileWriter.findUniqueFileName(filename, targetDirectory);
+                FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
+                return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
             }
             catch (ExperimentException e)
             {
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java b/laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java
index 731216b4..6e55124b 100644
--- a/laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java
+++ b/laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java
@@ -56,6 +56,7 @@
 import org.labkey.laboratory.assay.AssayHelper;
 import org.labkey.laboratory.query.DefaultAssayCustomizer;
 import org.labkey.laboratory.query.LaboratoryTableCustomizer;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.lang.reflect.InvocationTargetException;
@@ -197,10 +198,10 @@ public Pair<ExpExperiment, ExpRun> saveAssayBatch(List<Map<String, Object>> resu
 
         try
         {
-            File targetDirectory = AssayFileWriter.ensureUploadDirectory(ctx.getContainer());
-            File file = AssayFileWriter.findUniqueFileName(basename, targetDirectory);
+            FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(ctx.getContainer());
+            FileLike file = AssayFileWriter.findUniqueFileName(basename, targetDirectory);
 
-            return this.saveAssayBatch(results, json, file, ctx, provider, protocol);
+            return this.saveAssayBatch(results, json, file.toNioPathForRead().toFile(), ctx, provider, protocol);
         }
         catch (ExperimentException e)
         {
diff --git a/laboratory/src/org/labkey/laboratory/assay/AssayHelper.java b/laboratory/src/org/labkey/laboratory/assay/AssayHelper.java
index 11367e31..528fe33a 100644
--- a/laboratory/src/org/labkey/laboratory/assay/AssayHelper.java
+++ b/laboratory/src/org/labkey/laboratory/assay/AssayHelper.java
@@ -29,6 +29,7 @@
 import org.labkey.api.assay.AssayService;
 import org.labkey.api.cache.CacheManager;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
+import org.labkey.api.collections.CollectionUtils;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.RuntimeSQLException;
@@ -58,6 +59,8 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.laboratory.LaboratoryController;
 import org.labkey.laboratory.LaboratorySchema;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.beans.Introspector;
 import java.io.File;
@@ -88,9 +91,8 @@ public static AssayHelper get()
         return _instance;
     }
 
-    public Map<String, File> saveResultsFile(List<Map<String, Object>> results, JSONObject json, File file, AssayProvider provider, ExpProtocol protocol) throws ExperimentException, ValidationException
+    public Map<String, FileLike> saveResultsFile(List<Map<String, Object>> results, JSONObject json, File file, AssayProvider provider, ExpProtocol protocol) throws ExperimentException, ValidationException
     {
-        Map<String, File> files = new HashMap<String, File>();
         //TODO: consider adding as input??
         //files.put("RawInput", file);
 
@@ -111,8 +113,8 @@ public Map<String, File> saveResultsFile(List<Map<String, Object>> results, JSON
             throw new ExperimentException(e.getMessage());
         }
 
-        files.put(AssayDataCollector.PRIMARY_FILE, newFile);
-
+        Map<String, FileLike> files = CollectionUtils.enforceValueClass(new HashMap<>(),FileLike.class);
+        files.put(AssayDataCollector.PRIMARY_FILE, FileSystemLike.wrapFile(newFile));
         return files;
     }
 
@@ -209,7 +211,7 @@ public Pair<ExpExperiment, ExpRun> saveAssayBatch(List<Map<String, Object>> resu
             });
         }
 
-        Map<String, File> uploadedFiles = saveResultsFile(results, json, file, provider, protocol);
+        Map<String, FileLike> uploadedFiles = saveResultsFile(results, json, file, provider, protocol);
 
         //TODO: see AssayRunAsyncContext
         AssayRunUploadContext uploadContext = new RunUploadContext<>(protocol, provider, name, comments, runProperties, batchProperties, ctx, uploadedFiles);
@@ -243,10 +245,10 @@ private File getUniqueOutputName(File input, String extension)
         File parent = input.getParentFile();
         String basename = FileUtil.getBaseName(input);
         int suffix = 1;
-        File newFile = new File(parent,  basename + "." + extension);
+        File newFile = FileUtil.appendName(parent,  basename + "." + extension);
         while (newFile.exists())
         {
-            newFile = new File(parent,  basename + "-" + suffix + "." + extension);
+            newFile = FileUtil.appendName(parent,  basename + "-" + suffix + "." + extension);
             suffix++;
         }
         return newFile;
diff --git a/laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java b/laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java
index cc1dbc73..4ce1f0d5 100644
--- a/laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java
+++ b/laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java
@@ -22,6 +22,7 @@
 import org.labkey.api.assay.AssayRunUploadContext;
 import org.labkey.api.assay.AssayService;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
+import org.labkey.api.collections.CollectionUtils;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpProtocol;
@@ -32,8 +33,8 @@
 import org.labkey.api.security.User;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewContext;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
@@ -53,9 +54,9 @@ public class RunUploadContext<ProviderType extends AssayProvider> implements Ass
     private final ViewContext _ctx;
 
     private TransformResult _transformResult;
-    private final Map<String, File> _uploadedData;
+    private final Map<String, FileLike> _uploadedData;
 
-    public RunUploadContext(ExpProtocol protocol, ProviderType providerType, String name, String comments, Map<String, String> runProperties, Map<String, String> batchProperties, ViewContext ctx, Map<String, File> uploadedData)
+    public RunUploadContext(ExpProtocol protocol, ProviderType providerType, String name, String comments, Map<String, String> runProperties, Map<String, String> batchProperties, ViewContext ctx, Map<String, FileLike> uploadedData)
     {
         _protocol = protocol;
         _providerType = providerType;
@@ -64,7 +65,8 @@ public RunUploadContext(ExpProtocol protocol, ProviderType providerType, String
         _runProperties = new CaseInsensitiveHashMap<>(runProperties);
         _batchProperties = new CaseInsensitiveHashMap<>(batchProperties);
         _ctx = ctx;
-        _uploadedData = uploadedData;
+        _uploadedData = CollectionUtils.checkValueClass(uploadedData, FileLike.class);
+        CollectionUtils.checkValueClass(_uploadedData, FileLike.class);
     }
 
     @Override
@@ -154,7 +156,7 @@ public ActionURL getActionURL()
 
     @Override
     @NotNull
-    public Map<String, File> getUploadedData() throws ExperimentException
+    public Map<String, FileLike> getUploadedData() throws ExperimentException
     {
         return _uploadedData;
     }