There are several options:
- You can use the L2 with surface reflectance already calculated. Level-2 products consist of geophysical quantities derived from the processing of measurement data provided in the Level-1 product. Level-2 products specifically for marine (EUMETSAT) and land (ESA) application domains are generated separately, with each containing the parameter relevant for the specific field of application. Level-2 atmospheric information relevant for both application domains, such as water vapour, is reported in both data streams
- If you are going to work on ocean, SNAP provides the C2RCC process to derive atmospherically corrected bands and OC concentrations.About cloud flagging, you can also find the IdePix tool in SNAP.
Some references in this Froum. Please make a further check:
Batch process subset, idepix, c2rcc on OLCI - #19 by marpet
Idepix for S3 OLCI via gpt?
OLCI C2RCC processing