System level tools based on MATLAB/Simulink are becoming popular for designing applications using FPGAs. In these tools, application designers describe their designs at high level using the powerful modeling environment provided by MATLAB/Simulink. Then, these designs are automatically translated into corresponding FPGA implementations. However, there is a lack of support for developing parameterized and energy efficient designs using these tools. In this paper, we propose PyGen, an add-on tool, to address this issue. The four major functionalities offered by our tool are: development of parameterized designs; integration of a domain-specific modeling technique for rapid and accurate energy estimation; profile of energy dissipation and feedback to application designers; flexible interface for design space traversal and identification of energy efficient designs. To illustrate the design process using the tool and to show its effectiveness, details of designs for an FFT kernel and an adaptive beamforming application are shown. For the adaptive beamforming application, the identified design achieves up to 30% energy reduction compared with other designs considered in our experiments.