You can still use split(), you just have to get a bit creative:

$str = 'c:\temp\source\test\test.c@@main\com\etc c:\temp\source\test\t
+est1.c@@main\com\test c:\temp\source\test\test3\test2.c@@main\com\etc
+\test';

print map {"$_\n" if s/c:\\temp(.*?\.c)/$1/} split(/\s+|\@+/,$str);
[download]

UPDATE: Thanks to Grandfather for the heads up on interpolation of my \'s. I did this correctly in my tests, but posted it wrong...thanks again.

SECOND UPDATE: I don't what happened between testing and posting that this code isn't working. It worked fine on my box.

THIRD AND (hopefully) FINAL UPDATE: Got it now. Thanks again to Grandfather.