In this paper, the energy losses in a one kilo-Watts two-stroke Linear Engine Alternator due to the application of flexural spring has been studied. Using flexural springs is a key factor for enhancing the efficiency and lifespan in linear applications e.g. linear engines, cryocoolers, Stirling engines. The energy loss due to vibrations and windage effects of Flexural springs in a free piston linear engine alternator with natural gas fuel has been investigated. Using Flexural springs eliminates the conventional bearings in the alternator and generates higher frequencies compared to conventional coil springs. However improper design would lead to a high amount of losses in flexures. A transient finite element solver has been used to find out the effects of higher modes of frequencies and vibrations of the arms of flexures at a certain operational frequency of 70 Hz. Also, a CFD solver has been utilized to understand the effects of drag force on moving surfaces of flexures at high frequencies. The numerical results were compared to experimental results obtained from damping tests and steady state test in the vacuum chamber. Results are in good agreement with experiment and shows between 20-50 Watts of energy loss at 70Hz in a one kilo-Watt alternator. An empirical formula has been introduced to estimate the windage losses based on the geometrical specifications of flexures and operational conditions including stroke length and frequency.