This study developed an optimisation method that considers tumour thickness for modulated electron radiation treatment (MERT) at a treatment distance of 60 cm. It comprises forming a tumour bed matrix from which a transformed tumour bed matrix is derived. From the discrete tumour bed depth data, electron beam segments were extracted, which were further decomposed into sub-beams. The EGSnrc-based Monte Carlo codes BEAMnrc and DOSXYZnrc were used to model a linear accelerator and to score 3-D dose data for various field sizes (sub-beams) in a water phantom model. The use of different energy and intensity-modulated electron sub-beams to irradiate a parotid lesion was investigated by applying the developed optimisation method. After each sub-beam energy was determined, a least square cost function minimisation was invoked to deliver a minimum dose to the tumour volume and produce a set of weight factors synonymous with beam intensity modulation. This study describes a technique to derive apertures and suitable sub-beam energy to provide a method for planning a robust MERT technique that yields dose-covering results and dose spread within the tumour that aligns with literature studies.