Your code doesn't compile:

$ perl -cw 1152653.pl
Global symbol "$in" requires explicit package name at 1152653.pl line 
+9.
Global symbol "$in" requires explicit package name at 1152653.pl line 
+11.
Missing right curly or square bracket at 1152653.pl line 14, at end of
+ line
syntax error at 1152653.pl line 14, at EOF
1152653.pl had compilation errors.
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You'll need to fix the errant opening brace and the scoping of $in.

Update: Here's a working rewrite of your script above:

use strict;
use warnings;
open my $in, '<', '1.txt' or die "Cannot open 1.txt: $!";
while (my $file = <$in>) {
    $file =~ s/..![^!]*something.*\.c//;
    print $file;
}
close $in;
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And here's what happens when I run it:

$ cat 1.txt
foo
?!?!?!/pack/something/whatever.cacshdska
bar
$ perl fixup.pl 
foo
?!?acshdska
bar
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