#slurp the files into arrays
open(FILE, 'filename_1');
@LINES_1 = <FILE>;
close(FILE);
open(FILE, 'filename_2');
@LINES_2 = <FILE>;
close(FILE);
open(FILE, 'filename_3');
@LINES_3 = <FILE>;
close(FILE);

# cycle through your file, pushing lines onto other files' arrays
for $i (0 .. $#LINES_1) {
     if (condition_a) {push(@LINE_2, $LINES_1[$i]);}}
     if (condition_b) {push(@LINE_3, $LINES_1[$i]);}}
}

# write new arrays to files
open(FILE, ">filename_2");
for my $i (0 .. $#LINES_2) {print FILE "$LINES_2[$i]";}
close(FILE);
open(FILE, ">filename_3");
for my $i (0 .. $#LINES_2) {print FILE "$LINES_3[$i]";}
close(FILE);