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Local synthesis and direct integration of Carbon Nanotubes (CNTs) with Si microstructures at room temperature has opened the prospects of a low-cost, wafer-level and CMOS-compatible processing of CNT-based devices. However, the performance of such devices depends upon the quality of CNTs and the contact between CNTs and the silicon structure. Therefore, the defects of CNTs and the CNT-silicon contacts need to be examined. In this paper, Scanning Electron Microscopy (SEM) observations are reported. Three types of CNT defects were observed: voids, branches, and coating flakes. The varying density and diameter distribution of CNTs grown along the microstructure were also revealed. The observations provide a better understanding of the local synthesis process.