How do I remove  from the beginning of a file?

Three words for you:

Byte Order Mark (BOM)

That’s the representation for the UTF-8 BOM in ISO-8859-1. You have to tell your editor to not use BOMs or use a different editor to strip them out.

To automatize the BOM’s removal you can use awk as shown in this question.

As another answer says, the best would be for PHP to actually interpret the BOM correctly, for that you can use mb_internal_encoding(), like this:

 <?php
   //Storing the previous encoding in case you have some other piece 
   //of code sensitive to encoding and counting on the default value.      
   $previous_encoding = mb_internal_encoding();

   //Set the encoding to UTF-8, so when reading files it ignores the BOM       
   mb_internal_encoding('UTF-8');

   //Process the CSS files...

   //Finally, return to the previous encoding
   mb_internal_encoding($previous_encoding);

   //Rest of the code...
  ?>