Depending on the type of interference, you may be able to apply a fast Fourier transform mask (this screens out the particular frequencies that are causing interference). I have done this using the software imageJ very simply, you can see an example here: https://imagej.nih.gov/ij/docs/examples/FFT/part2.html

Natalie Laura Garrett I can only warn to abstain from such practices to "correct" spectra. Removing fringes by FFT heals only one sympton, but not the "disease", which consists in increased/decreased absorption due to interference enhancement/decrease (see Fabry-Perot effect, Etaloning, Electric field standing wave effect etc.) See e.g. Article The electric field standing wave effect in infrared transfle...

Article The Electric Field Standing Wave Effect in Infrared Transmis...

The only option is to remove the fringes by wave-optics conform solutions like e.g. RefFIT by Alexey Kuzmenko (https://reffit.ch/) or CODE by Wolfgang Theiss (https://www.wtheiss.com/) and SpIRIT by Konstantin Shportko (http://www.shportko.com/spirit.html). Alternatively you can also use the formalism suggested in Article Removing interference-based effects from the infrared transf...

Cavity affects arise when there is high reflection at parallel boundaries, and low absorption. The more those conditions are met, the higher the "Q" and the deeper the depth of modulation.

Does your interference come the sample or the detector?

If from the sample, then you can consider tilting the source some amount and take new data. Also, if you can make the sample thicker, or remove whatever is reflecting from the back side of the sample, then that should help. If the sample is high index of refraction then doing some type of AR coating or index matching medium will also help.

If the pattern is from a back illuminated CCD, then you can check if vertical binning of the image pixels will help average it out. I have only read about that affect and that is the solution that folks suggest.

If your data, which is now months old cannot be re-taken, and you must work with the spectrum you have, then I like Natalie Laura Garrett 's idea of a FT filter since the pattern likely has a narrow frequency range. ImageJ is free to download and use from the U.S. National Institute of Health.

If the interference does not look sinusoidal, AND your spectrum does not have any actual high frequency components then you can do a type of low pass filter. There are a few different ways to do that.

Dear Tharith Sriv. For beginners (as we are) to remove interference patterns the best way is to apply Fourier transform to spectra. Then you remove the peak related to interference and apply inverse Fourier transform. Both procedures are standard in FTIR spectrometers soft. Just try it.

Thank you, Natalie Laura Garrett , Thomas Mayerhöfer , Mark Schnittker and E. Vasil'ev for your kind suggestions. I'm going to carefully try what have been suggested.