Hello @shubham_prajapati,
If you want to keep only one variant, then you can remove unused post-build variant ref:

However, my understanding is you want to remove the whole variant concept (as a result the configuration file name will not contain the variant name, e.g. Mcu_PBCfg.c instead of Mcu_PBCfg_VS_0.c). In that case, it would be more complicated, and as my experience, here are the steps I often do:
1. Export the configuration from the variant which I want to keep to .epc files
2. Emove all of the modules and the .xdm files
3. Re-add all of the modules
4. Import the .epc files from step 1.
Best Regards,
Nam