Free electron lasers (FELs) are becoming more and more popular as sources of radiation for research purposes in many fields of science. They are frequently employed in second harmonic generation (SHG) studies. SHG is an important effect of nonlinear responses of matter to irradiation. It should be separated from the second harmonic of the radiation source, FELs, for correct analysis of the response. Using an analytical model for harmonic powers evolution in a single-pass FEL, we demonstrate the dependence of FEL harmonics on the key parameters of beams and undulators and show that it is possible to reduce the second FEL harmonic content if the energy spread of an electron beam is increased. For LEUTL FEL radiation in the visible range, we analytically demonstrate a reduction in the second harmonic power by an order of magnitude if electron energy spread is increased twice, which still allows efficient bunching at the fundamental wavelength. The method is valid regardless of the photon energy and, therefore, the absorption edge of the target material, and as such, it is valid also in the X-ray band.