In this work, we have synthesized and well-characterized a library of anti-M6PR antibody conjugated fluorescent and biodegradable nanoPMOs with varied sizes, shapes, compositions, orientations, and multivalency in order to investigate their physicochemical properties predominantly biodegradability and surface functionality by super-resolution dSTORM imaging modality for effective stimuli-responsive drug delivery for targeted chemotherapy of prostate cancer. In dSTORM imaging with nanometric spatial resolution (around 20 nm), we have quantified the biodegradation of various nanoPMOs, which was unprecedented and found that their excellent degradation behavior depends on their structural characteristics. A single particle level analysis of nanoPMOs conjugated with an anti-M6PR antibody has revealed that one of the most important parameters, namely the surface functionality of nanoPMOs, such as the number, distribution, and density of antibody per nanoparticle, shows a significant impact on prostate cancer cell targeting using dSTORM imaging. Aside from the surface functionality of nanoPMOs, the size, and shape of nanoPMOs also significantly influence their interaction with living cells, leading to variations in cellular uptake by healthy and cancerous prostate cells. According to the results, small-sized nanorods functionalized with oriented antibody have higher M6PR overexpressed prostate cancer cell labeling capabilities when they are functionalized at high density, whereas heterogeneous surface functionality reduces the ability of nanoPMOs with low multivalency to bind to cancer cells. The excellent hydrophobic drug loading capacity of nanoPMOs into the porous structure, and glutathione-triggered controlled drug release properties could improve the effectiveness of highly biodegradable nanoPMOs, which exhibit better cancer cell targeting ability in targeted chemotherapy of prostate cancer, resulting in the potent anticancer activity of EAB4H nanorods with low lethal concentrations (LC50).