A two-step self-assembly procedure on smooth, aminated silica particles established holey monolayers. At first, single, flat-lying porphyrin tetraamides (A) were bound covalently, followed by the build-up of a rigid monolayer made of diamido bolaamphiphiles (bolas) around the porphyrin islands. "Nanowells" around porphyrin (A) bottoms with a uniform diameter of 2.2 nm and varying depths of 0.6, 1.0, or 1.5 nm depending on the length of the applied bolas were thus obtained. Oligoethylene headgroups solubilized the particles in water, ethanol, and chloroform/ethanol, and two hydrogen bond chains between the secondary amide groups prevented swelling of the monolayer. Manganese(III) porphyrinates (B) migrated from the bulk solution to the bottom of the form-stable nanowells with a speed of about 1 pm/s and were trapped there above porphyrin (A). After isolation of the (A,B) particles by centrifugation or ultrafiltration, the particles were suspended in a chloroform solution of a chlorin (C), which was also fixated irreversibly on the bottom of the nanowells. The nanowells thus contained three different porphyrins A,B,C in a noncovalent stack. The reverse sequence A,C,B was built-up correspondingly, first in chloroform/ethanol, and then in water. The "sorting" of A,B,C and A,C,B systems was characterized by visible spectra, sequence-dependent fluorescence quenching, and cyclic voltammetry of the top component. The molecular sorting method is the first of its kind and should be generally useful for the production of noncovalent reaction systems on any smooth surface.