Spatial fractionation of radiation using arrays of narrow parallel micro-planar beams (less than 1 mm), is a relatively new concept with many unknowns specifically within the underlying biology of cell death. A tungsten collimator has been designed to produce mini-beams with a Varian linear accelerator for translational animal research into the effectiveness of spatial fractionation mini-beam radiotherapy (MBRT). This work presents the treatment planning process and workflow for the application of MBRT treatments within a clinical study. For patient dose calculations, the MBRT collimator was incorporated into a Monte Carlo based treatment planning system called MMCTP. Treatment planning was split between Eclipse and MMCTP, as the field apertures were determined within Eclipse prior to being sent to MMCTP for dose calculations. The calculated plan was transferred back into Aria with updated MUs per field for patient treatment. Patients were positioned within a vac-lock bag lying prone with a bite block and a thermoplastic mask to immobilize the head. Prior to treatment, a delivery verification plan was created within MMCTP. DQA output measurements of the treatment fields agreed with the calculated dose to within 1.5%. We have presented a workflow for MBRT treatments that include the planning technique, dose calculation method, DQA process and data integration into a record and verify system. The clinical study following this workflow represent the first series of linac based MBRT patients and depending on the clinical outcome of the study, our technique could be applied to human MBRT treatments.