Prostate cancer (CaP) is the commonest diagnosed malignancy and the second main cause of cancer mortality in males in the United States. Thus, there is an urgent need to develop novel drug delivery systems to improve the chemotherapy option for CaP patients. The goal of this paper is to describe novel moleculary guided nanoscale drug delivery system with dual functionality for treatment and MR imaging of CaP. We describe the synthesis of iron oxide nanoparticles (IONPs) which are then coated with carboxyl-ended amphiphilic polymer. We present the protocol for tethering of the CaP targeting protein, human amino terminal fragment (hATF) to the terminal carboxyls of the IONPs. We describe the drug loading and release and the methods for measuring of the internalization of the hATF-guided IONPs into CaP cells. We also describe the methods for usages of IONPs are MR imaging contrast agent and successful targeted drug carriers.