map returns the value of the last expression evaluated within { #block }. The last expression you're evaluating is a substitution operator, and its value is a boolean value; true (1) if a match occurred, or false if there was no match. That's why it keeps passing '1' into @nar. If you want to return the result of the substitution, make sure that value is the last thing evaluated in { #block }.

@nar = map { # get rid of trailing number
             my $st = ( split( " ", $_ ) )[0];
             # replace bracket with S
             $st =~ s/\[[ATCG]+\/S/g;
             # return result value
             $st;
       } @arr;
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...that ought to do it...