G'day BernieC,

Regex issues:

• Your first regex, s/^\xef\xbb\xbf//g, anchors to the start of the string: later ef bb bf sequences will not be removed.
• Your second regex, s/\xef\xbb\xbf//, has no /g modifier: only the first ef bb bf sequence will be removed.

What you need is s/\xef\xbb\xbf//g:

$ perl -Mstrict -Mwarnings -E '
    my $x = "\x{ef}\x{bb}\x{bf}123,,,\x{ef}\x{bb}\x{bf}456";
    say "Full string:";
    system "echo $x | hexdump -Cv";

    $x =~ s/\xef\xbb\xbf//g;
    say "All BOM sequences removed:";
    system "echo $x | hexdump -Cv";
'
Full string:
00000000  ef bb bf 31 32 33 2c 2c  2c ef bb bf 34 35 36 0a  |...123,,,
+...456.|
00000010
All BOM sequences removed:
00000000  31 32 33 2c 2c 2c 34 35  36 0a                    |123,,,456
+.|
0000000a
[download]

To remove other characters:

• Non ISO-8859-1: y/\x00-\xff//cd
• Non 7-bit ASCII: y/\x00-\x7f//cd