Production of self-assembled defect structure via aggregation of molecules is one of the key issues in advanced nanotechnologies. Use of top-down lithographic template helps not only to define size and shape of defect but also to range defect domains periodically. Recently, it has been successfully achieved to realize periodic dimple-shaped TFCD (Toric Focal Conic Domain) array by confining fluorinated smectic liquid crystal into microchannel template. Here we demonstrate highly ordered defect arrays using liquid crystals having chiral phase confined in rectangular channels. Unlike previous TFCD that is formed in SmA phase, TFCD with chiral SmC phase shows distinct spiral shape under polarized optical microscopy (POM). Movement of spiral arms of each domain has been observed under electric field. Such movement is presumed to be related to the deformed helix ferroelectric (DHF) effect caused by unwinding tendency of helical axis under electric field perpendicular to the axis. We further apply various kinds of field geometry to examine mechanism of topological deformation of TFCD.