A method of trimming FET NVM cells in Multi-Level-Cell (MLC) operation is provided. The method comprises (a) applying a first voltage and a second voltage to a control gate and a bulk of the over-programmed FET NVM cell, respectively; and (b) applying a signal to a drain of the over-programmed FET NVM cell for a time period to produce a limited threshold voltage reduction; wherein polarities of the first voltage and the second voltage are opposite to that of the signal. Thus, the charge placement in the storing material could be precisely controlled within a small range of charge state and produce a multi-bits/cell of higher digital storage density.