Various small molecules are used for imaging agents and medicines. Although their molecular properties such as spatial distribution in vivo are critical for the function, robust methods for evaluating them have been limited. Herein, we report a new method to trap and visualize exogenously administered molecules of interest (MOIs) in the brain. This method realizes to obtain images of the 3D distribution of the small molecules, which addresses selective/nonselective binding to proteins, time-dependent localization changes, and diffusion/retention kinetics of MOI.