Confidential projects and documents can be hidden from specified user groups by implementing a data field on the projects or documents 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, hover over Administration and select Filters. Select the user group you want to apply the filter to and click on the add button 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.