Sentinel-2 Level 2A clouds removal

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If you use L2A data, you already have a cloud mask available which you can use to exclude those pixels from further processing.

See here:

Ways of how to mask and remove clouds from Sentinel-2 Data?

sen2cor does not remove the clouds. It is doing an atmospheric correction and masks the clouds. You can use the scl_cloud_*_proba flags in the quality_scene_classification flag band or the value of quality_cloud_confidence to remove them on your own. For example, you can set the valid pixel expression of reflectance bands. However, cloud masking is not perfect. If you’re not satisfied you can check if Idepix for Sentinel-2 (also not perfect) fits your needs. It does the detection on an S2 L1C …

sen2cor is the processor used to generate L2A products.