In this paper, we present a new method for the design and implementation of modulated filter banks with perfect reconstruction. It is based on the decomposition of the analysis and synthesis polyphase matrices into a product of two different types of simple matrices, replacing the polyphase filtering part in a modulated filter bank. Special consideration is given to cosine-modulated as well as time-varying filter banks. The new structure provides several advantages. First of all, it allows an easy control of the input-output system delay, which can be chosen in single steps of the input sampling rate, independent of the filter length. This property can be used in audio coding applications to reduce pre-echoes. Second, it results in a structure that is nearly twice as efficient as performing the polyphase filtering directly. Perfect reconstruction is a structurally inherent feature of the new formulation, even for nonlinear operations or time-varying coefficients. Hence, the structure is especially suited for the design of time-varying filter banks where both the number of bands as well as the prototype filters can be changed while maintaining perfect reconstruction and critical sampling. Further, a proof effective completeness is given, and the design of equal magnitude-response analysis and synthesis filter banks is described. Filter design can be performed by nonconstrained optimization of the matrix coefficients according to a given cost function. Design and audio-coding application examples are given to show the performance of the new filter bank.