The LHC Low Level RF System (LLRF) is a complex multi-VME crate system which is used to regulate the superconductive cavity gap voltage as well as to lower the impedance as seen by the beam through low latency feedback. This system contains multiple loops with several parameters to be set before the loops can be closed. In this paper, we present a suite of MATLAB based tools developed to perform the preliminary alignment of the RF stations and the beginnings of a closed loop model based alignment routine. We briefly introduce the RF system and in particular the base band (time domain noise based) network analyzer system built into the LHC LLRF. The main focus of this paper is the methodology of the algorithms used by the routines within the context of the overall system. Measured results are presented that validate the technique. Because the RF systems are located in a cavern 120 m underground in a location which is relatively un-accessible without beam and completely un-accessible with beam present or magnets are energized, these remotely operated tools are a necessity for the CERN LLRF team to maintain and tune their LLRF systems in a similar fashion as to whatmore » was done very successfully in PEP-II at SLAC.« less