According to the surface characteristics of continuous phase plates with small feature structures on high surface gradients and extensive mid-to-high spatial frequencies, several factors influencing the machining accuracy of the phase plates are analyzed. These factors include raster scanning pitch, material removal programming, positioning precision and material removal. The analysis points out that the optimal pitch can be selected according to the Nyquist sampling theorem to achieve the effective imprinting of feature structures with different sizes. When the surface errors in all spatial frequency ranges are controlled effectively , the stable dwell time can be achieved during the raster scanning process by the optimized material removal programming. Furthermore, when the surface matching method is used to correct the measurement errors , the accurate material removal information can be obtained. When the positioning precision of the removal accuracy is increased, the machining accuracy of the element with small feature structures can be improved significantly. Finally, on the basis of eliminating of different process errors, the Ion Beam Fabrication(IBF) is adopted to imprint the complex phase structures with characteristic dimensions as small as 1.5 mm, surface peak-to-valley (PV) smaller than 200 nm and surface gradient as large as 1.8 μm/cm. The results show that the matching error between figured surface and desired surface has been controlled down to 8.1 nm (Root-Mean-Square, RMS) of design specifications. The experimental results verify the reliability of the error analysis.