Confidential projects and documents can be hidden from specified user groups by implementing a field on the entity called: Confidential. This should be a Yes / No field.
A user group filter should then be set up for the user groups who are not allowed to view confidential projects. To set up the user group filter go to Administration and click on the Filters icon. Select the user group you want to apply the filter to and click on the funnel next to the entity you want to set up the filter for:
The user group filter should then be set up as follows:
The above screenshot shows an example of a Project user group filter, but a similar filter can be set up to filter out confidential documents.