Sasidhar,
By your explanation I understand that you need to make a destination message from multiple schemas in mapper of BizTalk. You cannot open multiple source schemas when you make a map file, can open only one. The work around to this is, drop a transform shape in an orchestration, double click it to launch Tranform Configuration, Give the map an appropriate name, Leave the default checked New Map, In the Source Schema, choose all the source schemas you want, select the destination schema, there is a check at the bottom (Launch mapper when I click OK) leave that checked and click ok, You'd be presented with a mapper file with all the selected source schemas and one destination schema. From now onwards you can delete that shape from orchestration as your map is in-place.
Hope that helps,
Regards,
Sajid.