It was recently observed from empirical traffic data that by aggregating the highly scattered plots of flow versus density from individual loop detectors for city regions with homogeneous spatial distribution of congestion, the scatter significantly decreases and a well-defined Macroscopic Fundamental Diagram (MFD) exists between space-mean flow and density. This result can be of great importance to unveil simple perimeter control policies in such a way that maximizes the network outflow (trip endings). Single-region perimeter control might be sub-optimal if there is a significant number of destinations outside the region of analysis or if the network is heterogeneously loaded. This paper integrates an MFD modeling to perimeter and boundary control optimization for large-scale networks with multiple centers of congestion, if these networks can be partitioned into a small number of homogeneous regions. Perimeter control actions may be computed in real-time through a linear multivariable feedback regulator. The impact of the perimeter control actions to a three-region real urban network is demonstrated via micro-simulation. A key advantage of the proposed approach is that it does not require high computational effort and future demand data if the current state of each region can be observed.