diff --git a/src/Generator/CodeGenerator.cs b/src/Generator/CodeGenerator.cs
index 200e94c4..58101ace 100644
--- a/src/Generator/CodeGenerator.cs
+++ b/src/Generator/CodeGenerator.cs
@@ -26,40 +26,35 @@ namespace Cxxi
         {
             library = new Library(options.OutputNamespace, options.LibraryName);
 
-            var parserOptions = new ParserOptions
-                {
-                    Library = library,
-                    Verbose = false,
-                    IncludeDirs = options.IncludeDirs
-                };
-
             Console.WriteLine("Parsing code...");
 
-            foreach (var file in options.Headers)
-            {
-                string path;
+            var headers = new List<string>();
+            transform.SetupHeaders(headers);
 
-                try
-                {
-                    path = Path.GetFullPath(file);
-                }
-                catch (ArgumentException)
-                {
-                    Console.WriteLine("Invalid path '" + file + "'.");
-                    continue;
-                }
+            foreach (var header in headers)
+                ParseHeader(header);
 
-                var module = new TranslationUnit(path);
-                parserOptions.FileName = path;
+            foreach (var header in options.Headers)
+                ParseHeader(header);
+        }
 
-                if (!ClangParser.Parse(parserOptions))
+        void ParseHeader(string file)
+        {
+            var parserOptions = new ParserOptions
                 {
-                    Console.WriteLine("  Could not parse '" + file + "'.");
-                    continue;
-                }
+                    Library = library,
+                    Verbose = false,
+                    IncludeDirs = options.IncludeDirs,
+                    FileName = file
+                };
 
-                Console.WriteLine("  Parsed '" + file + "'.");
+            if (!ClangParser.Parse(parserOptions))
+            {
+                Console.WriteLine("  Could not parse '" + file + "'.");
+                return;
             }
+
+            Console.WriteLine("  Parsed '" + file + "'.");
         }
 
         public void ProcessCode()
diff --git a/src/Parser/Parser.cpp b/src/Parser/Parser.cpp
index 25e9509a..4d55b94b 100644
--- a/src/Parser/Parser.cpp
+++ b/src/Parser/Parser.cpp
@@ -19,6 +19,8 @@
 #include <clang/Driver/Util.h>
 
 #include <string>
+#include <iostream>
+#include <sstream>
 
 //-----------------------------------//
 
@@ -1315,16 +1317,15 @@ bool Parser::Parse(const std::string& File)
 
     C->setASTConsumer(new ParseConsumer());
 
-    // Get the file  from the file system
-    const clang::FileEntry* file = C->getFileManager().getFile(File.c_str());
+    // Create a virtual file that includes the header. This gets rid of some
+    // Clang warnings about parsing an header file as the main file.
 
-    if (!file)
-    {
-        Debug("Filename '%s' was not found.\n", File.c_str());
-        return false;
-    }
+    std::string str;
+    str += "#include \"" + File + "\"" + "\n";
+    str += "\0";
 
-    C->getSourceManager().createMainFileID(file);
+    auto buffer = llvm::MemoryBuffer::getMemBuffer(str);
+    C->getSourceManager().createMainFileIDForMemBuffer(buffer);
 
     clang::DiagnosticConsumer* client = C->getDiagnostics().getClient();
     client->BeginSourceFile(C->getLangOpts(), &C->getPreprocessor());