Comparisons of the focusing properties for the radially and azimuthally polarized beams with different pupil functions, such as uniform, Gaussian and Bessel-Gauss profiles, are presented. The results show that, for any pupil function, the spot sizes of the azimuthally polarized beam modulated with the vortex-0-2π-phase plate or the π-phase-step plate are smaller than that of the radially polarized beam encoded with or without these two types of plates. Then a type of multi-zone phase plate for generating tighter multifocal arrays from azimuthally polarized beams is proposed. The position and the linear polarization of the multifocal spots can be controlled by varying the pattern of the multi-zone phase plate and rotating the direction of the π-phase-step plate. In addition, for the radially polarized beam with Gaussian or Bessel-Gauss profiles and with the specified ratio of pupil diameter to beam diameter, the focal spot can be further reduced after modulated with the vortex-0-2π-phase plate, and the focal spot will be split into two after modulated with the π-phase-step plate. The latter property can be used to double the efficiency of parallel micro-manipulation.