Multilayer nanoscale systems incorporating ultrathin tunnel barriers, magnetic materials, amorphous oxides, and promising dielectrics are essential for next-generation logics, memory, quantum, and neuro-inspired computing. Still, an ultrathin film control at the atomic scale remains challenging. Here, we introduce a complementary metal-oxide semiconductor-compatible approach using focused ion beam irradiation for buried ultrathin films' engineering with subangstrom thickness control. Molecular dynamics simulations confirm the pivotal role of ion-induced crystal defects. Its performance is exemplified by Josephson junction resistance tuning in the range of 2 to 37% with a 0.86% standard deviation in completed chips. Furthermore, it enables ±17-megahertz frequency accuracy (±0.172 angstrom tunnel barrier thickness variation) in superconducting multiqubit processors, as well as qubit energy relaxation and echo coherence times exceeding 0.5 milliseconds.