This paper considers the two-dimensional electromagnetic scattering from periodic array of circular cylinders in which some cylinders are removed, and presents a formulation based on the recursive transition-matrix algorithm (RTMA). The RTMA was originally developed as an accurate approach to the scattering problem of a finite number of cylinders, and an approach to the problem of periodic cylinder array was then developed with the help of the lattice sums technique. This paper introduces the concept of the pseudo-periodic Fourier transform to the RTMA with the lattice sums technique, and proposes a spectral-domain approach to the problem of periodic cylinder array with defects.