Engineering inorganic nanoparticles with a biocompatible shell to improve their physicochemical properties is a vital step in taking advantage of their superior magnetic, optical, and photothermal properties as multifunctional molecular imaging probes for disease diagnosis and treatment. The grafting/peeling-off strategy we developed for nanoparticle surface coating can fully control the targeting capability of functional nanoprobes by changing their colloidal behaviors such as diffusion and sedimentation rates at the desired sites. We demonstrated that a cleavable coating layer initially immobilized on the surface of magnetic resonance imaging probes not only makes the nanoparticles water-soluble but also can be selectively removed by specific enzymes, thereby resulting in a significant decrease of their water solubility in an enzyme-rich environment. Upon removal of surface coating, the changes in hydrodynamic size and surface charges of nanoprobes as a result of interacting with biomolecules and proteins lead to dramatic changes in their in vivo colloidal behaviors (i.e., slow diffusion rates, tendency to aggregate and precipitate), which were quantitatively evaluated by examining changes in their hydrodynamic sizes, magnetic properties, and count rates during the size measurement. Because the retention time of nanoprobes within the tumor tissues depends on the uptake and excretion rate of the nanoprobes through the tumors, selective activation of nanoprobes by a specific enzyme resulted in much higher tumor accumulation and longer retention time within the tumors than that of the inactive nanoprobes, which passively passed through the tumors. The imaging contrast effect of tumors using activatable nanoprobes was significantly improved over using inactive probes. Therefore, the grafting/peeling-off strategy, as a general design approach for surface modification of nanoprobes, offers a promising and highly efficient way to render the nanoparticles suitable for targeted imaging of tumors.