The manufacturing process-caused variation in the modulus and the yield strength of individual layers in passivated metal stacks critically impacts the reliability of back-end-of-line (BEOL) structures. However, experimentally characterizing the elastic modulus and yield strength of thin films as fabricated, with sufficient sensitivity to distinguish process-induced property variations, remains a significant challenge. Towards this end, we utilize nanoindentation experiments to estimate the elastic modulus and yield strength of top-layer films in multilayer stacks. To address the challenge of extracting individual layer modulus from the composite modulus, in the present paper, we propose a depth-dependent mathematical model (dominant regime theory) by which the modulus of the top-layer can be estimated accurately. Additionally, we employ optimization-based inverse finite element analysis (IFEA) to numerically estimate the modulus and the yield strength of the top-layer film. The uniqueness of the properties estimated by IFEA is investigated through a full-factorial statistically designed numerical experiment. The developed techniques are demonstrated by estimating the modulus as well as the yield strength of tetraethylorthosilicate (TEOS) film on a two-layer stack (TEOS, Silicon) and the same film deposited on a multilayer stack (TEOS, Aluminum, Silicon Nitride, Silicon).