To remove modules from the "top menu" (I assume that this is the drop down list in the center of the control panel), then you have to uninstall the module.

If you want to have modules appearing in the list of modules that can be installed from the Host, Module Settings menu, you need to put their install zip files in the Install directory, and rename them from ModuleName.zip to ModuleName.resources.

For DotNetNuke modules, you can download the install zip files from DotNetNuke.com.

You can do this for ANY module, even purchased modules.