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I have a Sentinel-2A and I can't fully classify it beacause it's cloudy. I watched the Luca congedo YouTube tutorial but it is applied to the Level-1C data. And the cloudmasking plugin in used on Landsat data only.

How can I remove/ filter those clouds?

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Which Sentinel 2A products do you use? These directly from ESA or that ones which were created with Sen2Cor?

Sen2Cor output provides a cloud layer (e.g. "..._CLD_10m.jp2").

If you use that ones directly from ESA you can use the scene classification layer (e.g. "..._SCL_10m.jp2") or use other layers as proxy (Water Vapour or Aerosol Optical Thickness).

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I've worked with cloudy data in the past and the best way I've found to deal with clouds is below:

Depending on what type of clouds you have in your image this may or may not work. If they are small and scattered puffy clouds it should work.

I usually start off by classifying just the area with the clouds. Then when I am aggregating my classes I aggregate them into two classes. Class 1 has clouds and class 2 is everything else.

Then (I use a bitmap in PCI Geomatica) when I classify my entire image I will classify outside of my cloud classification. This way it will ignore the clouds and only classify the ground left around them.

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