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You can remove your custom, and user controls from the toolbox by just removing the corresponding line <toolboxControls> section in your web.cofig. For example if I have a user control called MyControl.ascx it will be added like this in the toolbox controls section:
| <add name="My Control" section="User Controls" url="~/UserControls/MyControl.ascx" />
All I need to do is remove that line. As for modules, you can prevent the CMS from loading modules (including built in ones), by just commenting/removing the lines that are referencing them.
You can also hide built in controls, to prevent them being used by users. For more information on how to do this, please take a look at the following article: How to hide controls from toolbox section in Sitefinity 3.6
I hope that this information helps you. If you have more questions, please feel free to contact us.
the Telerik team