Library Search Permissions

This is actually what makes SharePoint Search Great is that when a user is querying SharePoint, SharePoint search apply security trimming based on the user identity and permission level. This is why you will see certain user with custom permission or user with explicit permission get different result set. So the best way to do it is to start classifying your content and categorize them so you apply the permission easily. Sometimes, it is better to move content from one container to another (document library to another one or document library to another site or to its own site collection and maybe also create different result sources to get better search experience!)