1. A system for processing orders for at least one medical prescription comprising: a computer network; a computer processor connected to the network; storage and memory connected to the computer processor for storing orders, images of orders, and software modules; at least one scanner connected to the computer processor for scanning documents; communication link connected to the computer processor for communicating with users; at least one display connected to the computer processor for displaying order images; at least one protocol resolving database connected to the computer network; at least one facsimile machine in communication with the network; an image quality control processing module, stored in a computer readable storage media, said image quality control processing module executable in said computer processor, said image quality control processing module configured to determine whether the order of the at least one medical prescription requires conversion to an image, monitor the quality of images captures, selectively accept and/or reject images captured by said at least one scanner responsive to the monitored quality; an order header processing module, stored in a computer readable storage media, said order header processing module executable in said computer processor, said order header processing module configured to review and receive non-clinical data associated with said order; an order completion processing module, stored in a computer readable storage media, said order completion processing module executable in said computer processor, said order completion processing module configured to review and receive clinical data associated with said order; a protocol resolution processing module, stored in a computer readable storage media, said protocol resolution processing module executable in said computer processor, said protocol resolution processing module configured to resolve applicable protocols associated with said order; a doctor calls processing module, stored in a computer readable storage media, said doctor calls processing module executable in said computer processor, said doctor calls processing module configured to receive and process information regarding said order and determine whether the order requires at least one of communicating and transmitting the information with a prescriber to resolve a protocol; a command and control processing module, stored in a computer readable storage media, said command and control processing module executable in said computer processor, said command and control processing module configured to monitor and receive input to said system and to determine whether a prescription remains in any one of a plurality of system queues longer than a predefined value, wherein an alert notification is generated upon exceeding the predefined value.