Contrast agents have long helped researchers and physicians alike delineate boundaries, but new diagnostic information is always sought after. A new field of molecularly targeted CT agents hopes to fill this void and supply physicians with prognostic information to find better treatments for patients. Borrowing from drug delivery and design, nanoparticles and similar platforms are being explored to help visualize complex biologic processes with never before seen resolution and fidelity. We discuss the development of this field and feasibility of translating some of these prospects to the clinic. Advances in chemistry, molecular biology, and engineering have molded this field emphasizing the early detection and treatment of diseases at the molecular and cellular level. Myriads of nanomedicine platforms have been proposed and developed and tested in laboratories and in preclinical models. However, very few have been translated to clinical trials. It is therefore a critical issue to recognize the factors affecting their eventual application in human. Better understanding of biological and biophysical obstacles encountered by these agents is necessary. Toward this aim, we critically review our present understanding of the biological obstacles encountered by the nano-agents, which we hope will motivate more studies to tune these technologies for future translational and clinical applications.