For past decades Micro-System Technology (MST) has been developed and it has enabled fabricating the microcomponents on the micro-systems. In order to measure such microcomponents having micrometer-size shapes, a concept of nano-CMM was proposed. According to the concept, nano-CMM specifications are, for example, a measuring range is (10 mm)3 and accuracy is 50 nm. Then, we have proposed a laser trapping probe as a position detecting probe for nano-CMM. The laser trapping probe can be suitable to nano-CMM because of high sensitivity, an availability of a high spherical probe stylus and changeable properties. On the other hands, there are sources of uncertainties, one of them is the standing wave, and the influence is experimentally investigated. The results reveal the facts such as following. The standing wave obviously influences the behavior of the laser trapping probe sphere. The positional fluctuations by the standing wave proceed several hundreds nm, and the phenomenon appears with high repeatability. A size of the probe sphere can be a crucial parameter for reducing the influence of a standing wave. As another possibility of reducing the influence, on the inclined substrate the probe tends not to be affected by the standing wave. On the other hands, the standing wave influences the probe sphere beyond 100 mm far from the flat silicon substrate.