The sufficiency of accurate data is a core element in data-centric geotechnics. However, geotechnical datasets are essentially uncertain, whereupon engineers have difficulty with obtaining precise information for making decisions. This challenge is more apparent when the performance of data-driven technologies solely relies on imperfect databases or even when it is sometimes difficult to investigate sites physically. This paper introduces geotechnical property estimation from noisy and incomplete data within the labeled random finite set (LRFS) framework. We leverage the ability of the generalized labeled multi-Bernoulli (GLMB) filter, a fundamental solution for multi-object estimation, to deal with measurement uncertainties from a Bayesian perspective. In particular, this work focuses on the similarity between LRFSs and big indirect data (BID) in geotechnics as those characteristics resemble each other, which enables GLMB filtering to be exploited potentially for data-centric geotechnical engineering. Experiments for numerical study are conducted to evaluate the proposed method using a public clay database.