Embodiments provide a scheme for non-parametric PV-level modeling and an optimal read threshold voltage estimation in a memory system. A controller is configured to: generate multiple optimal read threshold voltages corresponding to multiple sets of two cumulative distribution function (CDF) values, respectively; perform read operations on the cells using a plurality of read threshold voltages; generate cumulative mass function (CMF) samples based on the results of the read operations; receive first and second CDF values, selected from among a plurality of CDF values, each CDF value corresponding to each CMF sample; and estimate an optimal read threshold voltage corresponding to the first and second CDF values, among the multiple optimal read threshold voltages.