Nanoheterostructures of NiSi/Si/NiSi in which the length of the Si region can be controlled down to 2 nm have been produced using in situ point contact reaction between Si and Ni nanowires in an ultrahigh vacuum transmission electron microscope. The Si region was found to be highly strained (more than 12%). The strain increases with the decreasing Si layer thickness and can be controlled by varying the heating temperature. It was observed that the Si nanowire is transformed into a bamboo-type grain of single-crystal NiSi from both ends following the path with low-activation energy. We propose the reaction is assisted by interstitial diffusion of Ni atoms within the Si nanowire and is limited by the rate of dissolution of Ni into Si at the point contact interface. The rate of incorporation of Ni atoms to support the growth of NiSi has been measured to be 7 × 10-4 s per Ni atom. The nanoscale epitaxial growth rate of single-crystal NiSi has been measured using high-resolution lattice-imaging videos. On the basis of the rate, we can control the consumption of Si and, in turn, the dimensions of the nanoheterostructure down to less than 2 nm, thereby far exceeding the limit of conventional patterning process. The controlled huge strain in the controlled atomic scale Si region, potential gate of Si nanowire-based transistors, is expected to significantly impact the performance of electronic devices.