The medicine dispensing system includes a plurality of storage containers for storing medical pills. The system also includes a hopper, a top and a bottom pre-fill tray, and a packing plate that are placed underneath each other respectively. Both the top and bottom pre-fill trays include a plurality of X-direction and Y-direction pointers.The system also includes a control module that uses feedback logic to align the top pre-fill tray with the bottom pre-fill tray using the X and Y direction pointers.In operation, the medicine dispensing system controls dispensing and navigation of pills from the storage container through the hopper, into the top pre-fill tray, into the bottom pre-fill tray, into the packing plate, and ultimately into a desired slot in the pill pack.The top and bottom pre-fill trays provide for separated compartmentalization of pills. This allows the medical pill dispensing system to parallel process and dispense pills designated for multiple pill packs at the same time without having to wait till the completion of any one pill pack. The separated compartmentalization ensures pills designated for one pill pack are not mixed with pills designated for another pill pack.