A position-based string can easily take substitutions using substr. Since you presumably know the positions and widths, you can say:

while (<$ifh>) {
    substr($_, $position, $width) =~ s/foo/bar/;
    print $ofh $_;
    # update $position and $width if necessary
}
[download]

Another approach is to unpack into an array or list of variables, make the modifications on those, and then pack back into a line to be printed to the output file.

Also, you can read a fixed-length chunk by setting local $/ = \42; (or whatever the record length is). That can be used to skip headers before the rest of the file is processed, too.

Update: Looking at the now-formatted data, I think I may have misunderstood what you meant by "position". Is this a CSV file? If so, follow that link.