The profile generation is highly complex for roughness measurement using a capacitive sensor because of the small peak-to-peak width of the machined surface and the close proximity of the sensor setting with the machining setup which has the chance of damaging the sensor. Considering these shortcomings, a higher sensor sensing diameter with an appropriate resolution has been selected for a single-shot approach. An automated micro gantry XYZ system is integrated with a capacitive sensor to precisely target, move, and measure the roughness. For investigation, a vertical milled surface with a wide roughness range has been prepared. A Stylus profilometer has been used to measure the roughness (Ra) of the specimens for comparison. An experiment has been conducted on the above system with a 5.6 mm capacitance sensor, and an estimation model using regression has been obtained using sensor data to estimate Ra. In conclusion, the single-shot approach with a 5.6 mm sensing diameter sensor, the proposed micro gantry system, and the estimation model performs better in instantaneous noncontact measurement in the range of 0.3 µm to 2.9 µm roughness estimation. The influence of tilt and waviness has also been discussed using FEA analysis.