The controller is configured to receive commands from a host device through a PCIe bus having a MAC, send data to the host device through the PCIe bus, and execute a function level reset (FLR) command. The controller includes a direct memory access (DMA) unit and either a drain unit or a drain and drop unit coupled between the DMA and the PCIe bus. The units are configured to prevent transactions associated with the FLR command to pass from the DMA to the MAC during execution of the FLR command, where the preventing transactions comprises receiving a request from the DMA, storing the request in a pipe, removing the request from the pipe, and providing a response to the DMA without delivering the request to the MAC. The drain and drop unit is configured to drop a MAC generated response.