Improved radiation therapy with field-in-field multi-leaf collimator, utilizing leaf sequencing Field-in-Field's (FIF) to accurately reproduce the input fluence map or original optimized dose distribution. The number of apertures used is constrained to a user-specified value all the way down to as few as 2 apertures which significantly magnifies the effect of poorly formed apertures. The disclosed invention further includes producing fluence maps with a homogenous dose throughout the treated volume utilizing leaf-sequencing Field-in-Field that reproduces more precise input fluence maps to yield optimized dose distribution.