Core-shell hybrid nanomaterials have shown new properties and functions that are not attainable by their single counterparts. Nanoscale confinement effect by porous inorganic shells in the hybrid nanostructures plays an important role for chemical transformation of the core nanoparticles. However, metal-organic frameworks (MOFs) have been rarely applied for understanding mechanical insight into such nanoscale phenomena in confinement, although MOFs would provide a variety of properties for the confining environment than other inorganic shells such as silica and zeolite. Here, we examine chemical transformation of a gold nanorod core enclosed by a zeolitic imidazolate framework (ZIF) through chemical etching and regrowth, followed by quantitative analysis in the core dimension and curvature. We find the nanorod core shows template-effective behavior in its morphological transformation. In the etching event, the nanorod core is spherically carved from its tips. The regrowth on the spherically etched core inside the ZIF gives rise to formation of a raspberry-like branched nanostructure in contrast to the growth of an octahedral shape in bulk condition. We attribute the shell-directed regrowth to void space generated at the interfaces between the etched core and the ZIF shell, intercrystalline gaps in multi-domain ZIF shells, and local structural deformation from the acidic reaction conditions.