A method and system for processing data by a storage controller with a buffer controller coupled to a buffer memory is provided. The method includes, evaluating incoming data block size; determining if the incoming data requires padding; and padding incoming data such that the incoming data can be processed by the buffer controller. The method also includes determining if any pads need to be removed from data that is read from the buffer memory; and removing pads from the data read from the buffer memory. The buffer controller can be set in a mode to receive any MOD size data and includes a first channel with a FIFO for receiving incoming data via a first interface. The buffer controller mode for receiving incoming data can be set by firmware.