Atomic layer deposition (ALD) in the presence of organic template molecules on substrates (molecular‐templated ALD) is a promising technique for designing a molecular selectivity with thermal robustness onto the surfaces of metal oxides, which are required for heterogeneous catalysts and molecular sensing. However, self‐aggregations of template molecules significantly impair the selectivity of the resulting molecules, which is difficult to prevent or observe. Here, a rational method is presented for uni‐molecularly dispersing template molecules and revealing their state in the molecular‐templated ALD process. The environment‐sensitive fluorescence of pyrene is utilized as a probe to visualize the microenvironments around template molecules. The dispersion of pyrene moieties in OH‐terminated SAMs allowed the pyrene molecules to be 1) covalently immobilized, 2) isolated from other pyrene molecules, and 3) surrounded by OH groups that act as ALD initiation sites. Systematic spectroscopic measurements of pyrene probes revealed the successful ALD of metal oxides surrounding template molecules without their undesired aggregations. Furthermore, emission enhancements are observed when Al2O3 is used as the surrounding metal oxide. The amplification of pyrene fluorescence intensity, lifetime, and quantum yield is attributed to the suppression of non‐radiative decay, indicating that the Al2O3 layer has grown closely around a single organic molecule.