Bottom-up fabrication of 3D organic nanostructures on Si(100) surfaces has been achieved by a two-step procedure. Tetradentate cavitand 1 was grafted on the Si surface together with 1-octene (Oct) as a spatial spectator by photochemical hydrosilylation. Ligand exchange between grafted cavitand 1 and self-assembled homocage 2, derived from cavitand 5 bearing a fluorescence marker, led to the formation of coordination cages on Si(100). Formation, quantification, and distribution of the nanoscale molecular containers on a silicon surface was assessed by using three complementary analytical techniques (AFM, XPS, and fluorescence) and validated by control experiments on cavitand-free silicon surfaces. Interestingly, the fluorescence of pyrene at approximately 4 nm above the Si(100) surface can be clearly observed.