Using the nano-composite deposition system (NCDS) as a microfabrication technique, implantable scaffolds were prepared with poly(DL-lactide-co-glycolide)(85:15) [PLGA(85:15)] as a biodegradable polymer. 5-Fluorouracil (5-FU) was used as a model drug, and hydroxyapatite (HA) was incorporated as a release modifier. In vitro drug release was evaluated and we confirmed that HA could control the release of drug from the prepared scaffolds, especially in the initial phase of the release. Furthermore, in vivo tests demonstrated that the microfabricated scaffold with pores was useful in reducing immune response and maintained its original shape, indicating that the drug delivery system was highly biocompatible.