diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
index af2758d1c..7b95b1653 100644
--- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
+++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
@@ -250,9 +250,9 @@ public class ValidationEngine implements IValidatorResourceFetcher {
 
   public class TransformSupportServices implements ITransformerServices {
 
-    private List<Resource> outputs;
+    private List<Base> outputs;
 
-    public TransformSupportServices(List<Resource> outputs) {
+    public TransformSupportServices(List<Base> outputs) {
       this.outputs = outputs;
     }
 
@@ -266,19 +266,13 @@ public class ValidationEngine implements IValidatorResourceFetcher {
     @Override
     public Base createType(Object appInfo, String name) throws FHIRException {
       StructureDefinition sd = context.fetchResource(StructureDefinition.class, name);
-      if (sd != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
-        return Manager.build(context, sd); 
-      } else {
-        if (name.startsWith("http://hl7.org/fhir/StructureDefinition/"))
-          name = name.substring("http://hl7.org/fhir/StructureDefinition/".length());
-        return ResourceFactory.createResourceOrType(name);
-      }
+      return Manager.build(context, sd); 
     }
 
     @Override
     public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
       if (atRootofTransform)
-        outputs.add((Resource) res);
+        outputs.add(res);
       return res;
     }
 
@@ -1210,13 +1204,13 @@ public class ValidationEngine implements IValidatorResourceFetcher {
     return issue.getSeverity().toString()+" @ "+issue.getLocation() + " " +issue.getDetails().getText() +(source != null ? " (src = "+source+")" : "");    
   }
 
-  public Resource transform(String source, String map) throws Exception {
+  public org.hl7.fhir.r5.elementmodel.Element transform(String source, String map) throws Exception {
     Content cnt = loadContent(source, "validate");
     return transform(cnt.focus, cnt.cntType, map);
   }
   
-  public Resource transform(byte[] source, FhirFormat cntType, String mapUri) throws Exception {
-    List<Resource> outputs = new ArrayList<Resource>();
+  public org.hl7.fhir.r5.elementmodel.Element transform(byte[] source, FhirFormat cntType, String mapUri) throws Exception {
+    List<Base> outputs = new ArrayList<Base>();
     
     StructureMapUtilities scu = new StructureMapUtilities(context, new TransformSupportServices(outputs));
     org.hl7.fhir.r5.elementmodel.Element src = Manager.parse(context, new ByteArrayInputStream(source), cntType); 
@@ -1224,13 +1218,12 @@ public class ValidationEngine implements IValidatorResourceFetcher {
     if (map == null)
       throw new Error("Unable to find map "+mapUri+" (Known Maps = "+context.listMapUrls()+")");
     
-    Resource resource = getTargetResourceFromStructureMap(map);
-
+    org.hl7.fhir.r5.elementmodel.Element resource = getTargetResourceFromStructureMap(map);
     scu.transform(null, src, map, resource);
     return resource;
   }
 
-  private Resource getTargetResourceFromStructureMap(StructureMap map) {
+  private org.hl7.fhir.r5.elementmodel.Element getTargetResourceFromStructureMap(StructureMap map) {
     String targetTypeUrl = null;
     for(StructureMap.StructureMapStructureComponent component: map.getStructure()) {
       if(component.getMode() == StructureMap.StructureMapModelMode.TARGET) {
@@ -1252,8 +1245,8 @@ public class ValidationEngine implements IValidatorResourceFetcher {
 
     if(structureDefinition == null)
       throw new FHIRException("Unable to determine StructureDefinition for target type");
-
-    return ResourceFactory.createResource(structureDefinition.getName());
+    
+    return Manager.build(getContext(), structureDefinition);
   }
 
   public DomainResource generate(String source, String version) throws Exception {
diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java
index 4a77c56dd..b175d8762 100644
--- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java
+++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java
@@ -537,11 +537,14 @@ public class Validator {
           throw new Exception("Must provide a map when doing a transform");
         try {
           validator.setMapLog(mapLog);
-          Resource r = validator.transform(sources.get(0), map);
+          org.hl7.fhir.r5.elementmodel.Element r = validator.transform(sources.get(0), map);
           System.out.println(" ...success");
           if (output != null) {
             FileOutputStream s = new FileOutputStream(output);
-            x.compose(s, r);
+            if (output != null && output.endsWith(".json"))
+              new org.hl7.fhir.r5.elementmodel.JsonParser(validator.getContext()).compose(r, s, OutputStyle.PRETTY, null);
+            else
+              new org.hl7.fhir.r5.elementmodel.XmlParser(validator.getContext()).compose(r, s, OutputStyle.PRETTY, null);
             s.close();
           }
         } catch (Exception e) {