We employed cobalt-disilicide for high-speed logic devices. We prepared stable and low resistant $CoSi_2$ through typical fabrication process including wet cleaning and rapid thermal process (RTP). We sputtered 15nm thick cobalt on the wafer and performed RTP annealing 2 times to obtain 60nm thick $CoSi_2$. We observed spherical shape voids with diameter of 40nm in the surface and inside $CoSi_2$ layers. The voids resulted in taking over abnormal junction leakage current and contact resistance values. We report that the voids in $CoSi_2$ layers are resulted from surface pits during the ion implantation previous to deposit cobalt layer. Silicide reaction rate around pits was enhanced due to Gibbs-Thompson effects and the volume expansion of the silicidation of the flat active regime trapped dimples. We confirmed that keeping the buffer oxide layer during ion implantation and annealing the silicon surface after ion implantation were required to prevent void defects in CoSi$_2$ layers.