This paper presents a multifunctional imaging system with a sensing unit including integrated microwave and laser sensors. It focuses on the development of software and algorithm for automated control of the movement of the sensing unit attached to the 3-axis scanning system and optimization of the standoff distance between the sensing unit and the material under test. The sensing unit consists of a microwave antenna/sensor and two laser displacement sensors. Microwave sensor is used for data acquisition and imaging of the surface and hidden flaws in the metal. Laser displacement sensors are used for obtaining profile information of the structure and an automatic adjustment of the sensing unit at optimized standoff distance. The optimization of standoff distance is important mainly in non-plain machine parts as their non-planarity might mask indications of minute flaws such as cracks. For this purpose, a combined software program is developed for data acquisition, motion control and synchronization in the LabVIEW platform. Further, the developed program includes a signal processing module for post-processing of signals and image smoothing. All these modules are synchronized using various functions with a trigger. A suitable user-friendly graphic user interface is also developed. The applicability of the system is demonstrated through a non-contact detection of hidden flaws in metals used in machine parts.