open(PREF,"+< preffile") or die;

while (<PREF>) {
    # if we see pref3 set to 0
    if (/^pref3\t0$/) {
        # you need to rewind two chars to get 
        # before the 0 and the newline , which 
        # you've already gone past
        seek(PREF,-2,1) or die;
        # print a "9" in this spot
        print PREF "9";
        # move forward one char past the newline
        # to continue reading.
        seek(PREF,1,1) or die;
    }
}
close PREF;