diff --git a/tools/Python/mcrun/mccode.py b/tools/Python/mcrun/mccode.py
index 064b55bb8..ae217f448 100755
--- a/tools/Python/mcrun/mccode.py
+++ b/tools/Python/mcrun/mccode.py
@@ -128,16 +128,21 @@ def x_path(file):
             ''' Return external path (relative to self.path) for file '''
             return '%s/%s' % (dirname(self.path), basename(file))
 
-        # Copy instrument file to cwd if not already there (for compatibility)
-        if not isfile(basename(self.path)):
-            shutil.copy2(self.path, ".")  # also copies stat information
-
         # Create the path for the binary
         if os.name == 'nt':
             self.binpath = '%s.%s' % (self.name, mccode_config.platform['EXESUFFIX'])
         else:
             self.binpath = './%s.%s' % (self.name, mccode_config.platform['EXESUFFIX'])
 
+        # Check if self.path is .exe or .out binary, if so - skip ahead to execution
+        if self.path==basename(self.binpath):
+            LOG.info('Called with binary file %s, skipping ahead to execution', self.binpath)
+            return
+
+        # Copy instrument file to cwd if not already there (for compatibility)
+        if not isfile(basename(self.path)):
+            shutil.copy2(self.path, ".")  # also copies stat information
+        
         # Check if c-code should be regenerated by comparing to instr timestamp
         existingC = findReusableFile(self.path,
                                      [self.cpath, x_path(self.cpath)])
diff --git a/tools/Python/mcrun/mcrun.py b/tools/Python/mcrun/mcrun.py
index 28e2f4936..2e74c84ce 100644
--- a/tools/Python/mcrun/mcrun.py
+++ b/tools/Python/mcrun/mcrun.py
@@ -444,12 +444,7 @@ def get_parameters(options):
 
 
 def find_instr_file(instr):
-    # Remove [-mpi].out to avoid parsing a binary file
     instr = clean_quotes(instr)
-    if instr.endswith("-mpi." + mccode_config.platform['EXESUFFIX']):
-        instr = instr[:-(5 + len(mccode_config.platform['EXESUFFIX']))]
-    if instr.endswith("." + mccode_config.platform['EXESUFFIX']):
-        instr = instr[:-(1 + len(mccode_config.platform['EXESUFFIX']))]
 
     # Append ".instr" if needed
     if not isfile(instr) and isfile(instr + ".instr"):