Removing clouds is not something easy to complete. Indeed when a cloud is present on an image it prevents the radiation to be transmitted. You could eventually mask them using the Masking tool in ENVI and process only area without clouds. Note also that you can find different approach in the literature to try to remove them:
Regarding atmospheric effects: there is an additional module to ENVI called ACM for Atmospheric Correction Module that allows to correct the effect of the atmosphere on the satellite images. If you are interesting in such tool feel free to contact your Sales representative for ENVI product family.
You can find more information about this module at the following page:
http://www.exelisvis.com/docs/AboutAt...