Replacing a magnetic atom by a spinless atom in a heavy-fermion compound generates a quantum state often referred to as a “Kondo-hole”. No experimental imaging has been achieved of the atomic-scale electronic structure of a Kondo-hole, or of their destructive impact [Lawrence JM, et al. (1996) Phys Rev B 53:12559–12562] [Bauer ED, et al. (2011) Proc Natl Acad Sci. 108:6857–6861] on the hybridization process between conduction and localized electrons which generates the heavy-fermion state. Here we report visualization of the electronic structure at Kondo-holes created by substituting spinless thorium atoms for magnetic uranium atoms in the heavy-fermion system URu₂Si₂. At each thorium atom, an electronic bound state is observed. Moreover, surrounding each thorium atom we find the unusual modulations of hybridization strength recently predicted to occur at Kondo-holes [Figgins J, Morr DK (2011) Phys Rev Lett 107:066401]. Then, by introducing the “hybridization gapmap” technique to heavy-fermion studies, we discover intense nanoscale heterogeneity of hybridization due to a combination of the randomness of Kondo-hole sites and the long-range nature of the hybridization oscillations. These observations provide direct insight into both the microscopic processes of heavy-fermion forming hybridization and the macroscopic effects of Kondo-hole doping.