Do you mean this program click here ? I haven't used it before, but here are the basics you need to know.
It depends on how the user name and password are stored, and what you choose to delete via the program.
If they are stored by way of a cookie, then yes (since cookies are one of the things cleaned up by the program), but you can configure it to keep the cookie from a particular website. This is probably what you're thinking about.
If you have stored the info in Internet Explorer's Autocomplete itself (Forms and Passwords), then possibly no, unless the program also deletes entries stored by IE's Autocomplete.
IE's AutoComplete stores 3 types of things, Web addresses, Forms and Passwords. If the program clears these out as well, and you're using IE's AutoComplete to remember your username and password, then make sure you don't clean out what you need to keep.