This paper develops a model-based hierarchical control method for coordinated ramp metering on freeway networks with multiple bottlenecks and on- and off-ramps. The controller consists of two levels where at the upper level, a Model Predictive Control (MPC) approach is developed to optimize total network travel time by manipulating total inflow from on-ramps to the freeway network. The lower level controller distributes the optimal total inflows to each on-ramp of the freeway based on local traffic state feedback. The control method is based on a parsimonious aggregated traffic model that relates the freeway total outflow to the number of vehicles on the freeway sections. Studies on aggregated traffic modeling of networks have shown the existence of a well-defined and low-scatter Macroscopic Fundamental Diagram (MFD) for urban networks. The MFD links network aggregated flow and density (accumulation). However, the MFD of freeway networks typically exhibits high scatter and hysteresis loops that challenge the control performance of MFD-based controllers for freeways. This paper addresses these challenges by modelling the effect of density heterogeneity along the freeway and capacity drop on characteristics of freeway MFD using field traffic data. In addition, we introduce a model to predict the evolution of density heterogeneity that is essential to reproduce the dynamics of freeway MFD accurately. The proposed model is integrated as the prediction model of the MPC in the hierarchical control method. The proposed coordinated ramp metering method shows desirable performance to reduce the vehicles total time spent and eliminate congestion. The control approach is compared with other coordinated ramp metering controllers based on the MPC framework with different traffic prediction models (e.g. CTM and METANET). The outcomes of numerical experiments highlight that the MFD-based hierarchical controller (i) is better able to overcome the modeling mismatch between the prediction model and the plant (process model) in the MPC framework and (ii) requires less computation effort than other nonlinear controllers.