A method of fabricating a multiple tunnel junction Scalable Two-Transistor Memory (STTM) cell array with a unit cell area as low as 4F2, F representing the minimum feature dimension, which usually is the width and also the spacing of the data lines or the write (or word or control gate) lines, wherein process sequence and conditions are designed to offer wide flexibility in material choices and layer thickness at different regions of the STTM cell with surface planarity maintained at several stages of the manufacturing sequence. The processing of memory cell devices is made compatible with peripheral CMOS devices so that the devices in both areas can be made simultaneously, thereby decreasing the total number of processing steps. Insulator filled trenches around the device regions, source/drain and the gate regions of the peripheral devices are formed simultaneously with the corresponding regions of the memory cell devices.