Upload Multiple Files With Multiple Fields And With media_handle_upload

I asked this question about few days ago and the answer solved my instantly problem but now when I tried to put many file fields in the form just the first field work because the solution of my previous question overwrite the $_FILES array.

Now I have the following HTML in my form:

<input type="file" name="my_file_upload[]" id="my_file_upload[]" multiple="multiple">
<input type="file" name="my_file_uploadone" id="my_file_uploadone">
<input type="file" name="my_file_uploadtwo[]" id="my_file_uploadtwo[]" multiple="multiple">

How can upload these files using media_handle_upload?

Any help will be appreciated.