Hi, there, I am a nonresident alien with H1B visa. I am filling up form 1040nr.

I could not find a place to deduct social security tax and medicare tax which were deducted in my paychecks.

There must be a place to deduct that amount, right? It does not make sense to pay federal tax on the amount of money I used to pay social security tax and medicare tax.

Appreciate any advice...

Why would you get a deduction for federal taxes you paid into social security and medicare?

Part of being here is paying the taxes, even if you probably won't benefit from social security or medicare, we all pay into them here, there's not a get out of some taxes free card because you came to the US and benefited from it but won't be staying forever.

On H1-B your income is subject to FICA taxes and you will not get any deduction for it even if it does not make any sense to you.

These are dual intend visas, that is a stepping stone to green card. So the visa holder gets same treatment as any other U.S. citizen or resident. If FICA taxes are not deducted form L1 and H1-B visa holders it becomes unfair to U.S. citizen or residents.
An other solution is that SS Administration finds a way to collect back FICA taxes with interest if a L1 or E3 visa holder gets green card.