Medical devices, such as stents, having a surface, a coating layer comprising a polymer disposed on at least a portion of the surface, and a composition comprising a biologically active material injected into or under the coating layer at one or more locations in the coating layer to form at least one pocket containing a biologically active material are disclosed. The composition may be injected using a nanometer- or micrometer-sized needle. Methods for making such medical devices are also disclosed. Using this method, a precise amount of the biologically active material may be disposed accurately and efficiently on the medical device at predefined locations.