Dear Kaushal
It is standard behavior of SAP that it costs all material inside the BOM while doing Costing run.
Please tick "DO NOT COST" check box in costing 1 tab of all RM (ROH) material master. And then run Standard Cost Estimate for your FERT or HALB materials. RMs will not be costed during run.
Don't worry their MAP will be considered in standard price calculation of FERT or HALB materials.
Regards
Rajneesh Saxena