qx("perl -p -i -e \"s/(\@Filetyp\\s*?:)/\\1$ext/\" /path/test.c")
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It is extremely rare that you need to call another perl from inside a Perl script! I'm going to guess that you're doing it for the effect of the -i flag? You can get that feature from inside Perl using $^I:

{ # new scope for local
    local *ARGV; @ARGV = '/path/test.c';
    local $^I = ""; # -i command line switch
    while (<>) {
        s/(\@Filetyp\s*?:)/$1 c/;
        print;
    }
}
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Update: qx// is often problematic anyway!

Update 2: Fixed this potential issue in the above example code.