To create a pattern that matches a string literally, use quotemeta, also available as \Q..\E.

my $f1 = <<'__EOI__';
//***********************************
//* Filename: Config1.c
//* Comment: [F1] is replaced by [F2]
//*
//***********************************
__EOI__

my $f2 = <<'__EOI__';
/***********************************/
/* Filename: Config2.c             */
/* Comment: [F2] replace [F2]      */
/*                                 */
/*                                 */
/***********************************/
__EOI__

s/\Q$f1/$f2/g;
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