This isn't fancy, but it will work,

for (@files) {
    open OLDDATA, "< $_"
        or warn 'File does not open: ', $! and next;
    open NEWDATA, "> $_!"
        or warn 'File not open: ', $! and next;

    while (<OLDDATA>) {
        s/aaaaa/FFFFFFF/gi;
        s/bbbbb/EEEEEEE/gi;
        s/cccccc/GGGGGGG/gi;
        print NEWDATA $_;
    }

    close NEWDATA or warn $! and next;
    close OLDDATA or warn $! and next;
    rename "$_!", $_;
}
[download]

This version is not much different from yours. It reads and processes the lines one at a time, instead of slurping to and array of lines. That will save memory by taking a smaller amount and reusing it. Efficient use of memory often increases speed in perl. Doing it that way requires a second file handle to write the lines to, so I opened a temporary file called "$filename!" to hold them. Once a file is done, rename does the file replacement very efficiently.

Beware that "$filename!" doesn't already exist. You probably won't have to worry about that if these files have some systemmatic naming, but if it's a problem the -e file test will help.

Update: The DATA filehandle is special to inlined data in perl. I changed the name.

After Compline,
Zaxo