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Modern Fourier transform microwave (FTMW) spectroscopy, first implemented as an impulse excitation technique in a steady gas-waveguide $apparatusa$, started only a quarter of a century ago. Soon after, the method was supplemented for special applications, e.g. Stark-$effectb$, double $resonancec$, and $2Dd$ spectroscopy. The subsequent implementation of the technique in a supersonic jet-resonator $apparatuse$ was followed by similar developments, i.e. Stark-$effectf$, double $resonanceg$, laser $ablationh$, and $DC-dischargei$. $Automationj$ along with the ``coaxially oriented beam-resonator $arrangement""k$ (COBRA) has greatly increased efficiency, resolution, and sensitivity of current FTMW spectrometers. We present the implementation of a complete COBRA-FTMW spectrometer featuring the capabilities given above. The entire experiment is operated, either interactivle or automatically, by a graphical user interface (GUI)-based program which is capable of waveguide and resonator applications. Developed in the C programming language, while following the concept of virtual instruments (VI), the software can co-operate with a wide variety of PCI and IEEE hardware components to build the instrument. Only one application specific logic circuit, which will also be presented, is needed.