when i search my web site on www.google.com i cant see my web site listed but when i search on www.google.com.np then i can see my site on the top of first page so what is the problem here
How are you searching for the site? It could be that it's not ranking well for the keyword you searched for.
Google has different data centers for different regions around the world, they are designed to show relevant search results in that region. This means that google.com can show different results than lets say google.co.uk, this is due to geographical differences. Use geo-targeting in Google Webmasters Central if you want to target a specific region.
I have not used that feature before. If you use it to target your geographic location will it hurt you in the wide world results?
I've never used it on a site or for a site that was already ranked well in other data centers; so I can't effectively answer this question. I would assume it wouldn't effect them, but again I have no live data to prove it. I've had a client site that I did this with not move in other data centers but one instance is not enough for me to give you the thumbs up.