We present a lowpass design algorithm targeted specifically for photonic implementation. Allpass filter based systems are ideal for photonic realizations because they can be naturally realized using a variety of nanoscale dielectric components. The allpass filters based lowpass system is a particularly noteworthy example of advanced usages of allpass sub-structures. While the structure is excellent for implementation using photonic components, practical considerations about its suboptimal performance are yet to be considered. Realistic optical filters are subject to the imperfections of photonic materials and limitations from current fabrication capability. The waveguide power loss is an unavoidable source of performance degradation that arises when realizing photonic filters. In this paper, we consider the derivation of allpass filters based lowpass structures that can minimize the loss effect. The proposed algorithm will enable the utilization of low cost photonic devices for stringent design requirements, and also improve the performance of high end photonic devices.