Use the Regex Feature of Find / Replace dialog box to find and remove non printable / non ASCII characters in your file using Notepad++.

Use the following string in Find what box:

[\x00-\x08\x0B\x0C\x0E-\x1F\x7F-\x9F]

Set the Search mode to Regular Expression, and leave Replace With as blank if you want to remove all the characters.