Yes you can cancel your fulfillment as long as they are running.  Once your fulfillment starts you'll see a cancel button to the far right of your fulfillment.  

Each file that is running will have a cancel button which will cancel the fulfillment for that specific file.  When you click the cancel fulfillment button you will be brought to a "confirmation" page which will ask you if you really want to cancel your fulfillment.

Click the Yes, I'm sure button to continue canceling your fulfillment.  Once you cancel the fulfillment, any orders that EZ Fulfill has not processed will be skipped and the process will complete.  The canceled fulfillment will show up in the Activity Log with a message letting you know the fulfillment was canceled and which orders have been processed and skipped.