A microcontroller system which employs an intermediate approach in hybrid FRAM-SRAM that involves memory mapping of program sections to retain the reliability benefits provided by FRAM while performing almost as efficiently as an SRAM-based system. They system utilizes an energy-aware memory mapping method which maps different program sections to the hybrid FRAM-SRAM MCU such that energy consumption is minimized without sacrificing reliability. The method comprises a memory initialization map, which performs a one-time characterization to find the optimal memory map for the functions that constitute a program. The method further comprises an energy alignment, a hardware/software method that aligns the system's powered-on time intervals to function execution boundaries, which results in further improvements in energy efficiency and performance.