Before you can upgrade your CRM 4 to 2011, you will need to uninstall all 3rd party addons and check that all buttons have been deleted. After the migration you can then install the latest version of each addon.
Should you have not done this, then it will be more complicated to get rid of the buttons and icons before you can install the CRM 2011 addons.
If you still have NavigationBar items which need to be removed, then you can do this by using the Forms customization option.
If you have Ribbon Buttons we recommend the following blog entries: http://dynamicscrm2011.wordpress.com/2011/04/05/ribbon-customization/
Another possibility to modify the ribbons gives you the Visual Ribbon Editor http://crmvisualribbonedit.codeplex.com/
or the Ribbon Workbench http://www.develop1.net/public/page/Ribbon-Workbench-for-Dynamics-CRM-2011.aspx
If you have SiteMap Buttons you want to remove, we can recommend the following blog entry with a description on how to modify the SiteMap in MS CRM 2011:
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