Please read instructions when posting -- they say "Put <code> </code> tags around your code and data!" (emphasis in the original text). Note that you can also use <c> and </c>, even within a paragraph.

Here's a demonstration to show how a regex substitution should work to remove null bytes:

s/\x00+//g;
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You can also use the "tr///" operator:

tr/\x00//d;   # a.k.a. "y///" : y/\x00//d;
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To see that in action, consider the following command lines, using perl one-liners (and assuming you have the "xxd" utility for doing a hex dump of stdin -- or some equivalent tool):

perl -e 'print "foo\x00bar"  | xxd -g 1
# produces this output (note the null byte):
0000000: 66 6f 6f 00 62 61 72                             foo.bar

perl -e 'print "foo\x00bar"  | perl -pe 's/\x00+//g' | xxd -g 1
# produces this output (no null byte):
0000000: 66 6f 6f 62 61 72                                foobar
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If you think you really are doing something like that, and it's not working for you, then you'll have to show a working demonstration of the code that proves it doesn't work.

My guess is you're doing something else wrong elsewhere in your code, unrelated to the regex. (If your program doesn't use strict; then it might be something as simple as a spelling error in a variable name.)