We consider that an ultracold two-level atom passes through multi spatially separated single-mode cavity fields and investigate the influence of the center-of-mass motion of the atom, the length of the cavity and the separation between two cavities on the transmission and photon emission probabilities of the atom. We find that both the transmission and photon emission probabilities as functions of the cavity length have multi-resonance peaks when the separation between two cavities is equal to an integer multiple of half the de Broglie wavelength of the atomic center-of-mass motion. The present work shows that the wave function of the atomic center-of-mass motion may be modulated in a macroscopic level by arranging the cavities.