1. Go to or send your parents/relatives to respective VDC or ward where you were born and request them to issue you a fresh official birth cert with your birth date, birth place and with parents full name on it. Nowadays most VDC issues the birth cert both in nepali and english on the same page. 

Thank you @DavilAngel. I am not sure if I can get number 2 or not.
I know most of us don't have birth registration. So any one with similar case , please share your experience.

As suggested by @DevilAngel, get all 3 as he suggested.
Getting the #2 is not difficult as u might have predicted. These days all VDCs and Municipalities have standard format for these. It does not matter if it is made in VDC or Municipality, current format of making Birth Certificate in English is more or less same across the country (Nepal).

Would a family relation document work as well? I have one of those made during the visa application with pictures of family and birth date with gov official signature and stamp.

The following is based on my personal experience. As you requested, I am sharing my experience, which may not be true for every individual.
Neither I nor my wife had the birth certificate. I had mine registered but could not find the original document. So I had my mom request a letter from the municipality (Nagarpalika). They gave me a typed document in the official letter head which is in English only and reads:
"This is to certify that xxxx, son of xxxx and xxxx, is a permanent resident of xxx, was born on mm/dd/yyyy A.D at xxxhospital according to his birth certificate #xxxxx"

That was it. No more documents were requested (regarding BC) and I have my GC now.

In my wife's case, she did not have her registration. Her dad went to the VDC and had them register then. They will use the actual "Janma Darta Praman Patra" template in Nepali, not just a letter as in my case. We used that in addition to its English translation and was accepted by USICS.

Hope this helps.

I been through similar situation twice with USCIS sending me RFE for Birth cert verification. Below is what I did and cleared the issue without any hiccups. Hope this helps for you.
- your first school from back home. Go there and ask them to write a letter in school pad saying "according to school record, this person is child of (your parents) and has birth date of xxxxxx"
- make a 2 copy of affidavt sample, and have them notarized.
(i have sample for them, if you want to send back home. I had hard time to make them understand the need to folks back there. so if you send sample, it helps).

include those 2 copies with below cover letter, you should be good.

(your address & email)
June 22, 2018

To,
USCIS/TSC
PO BOX 852381
Mesquite, TX 75185-2381

RE: Response to "Request for Evidence", File no: (USCIS SRC #)

Dear Sir/Madam:

In response to your "Request for Evidence", Please find the following documents enclosed herewith:

• The "Request for Evidence" letter and the envelope.
• Copy of " Early School Records" for (person name) showing the date of admission, place and date of birth including both parents name.
• Notarized copy of "affidavit letter" from 2 family friends and neighbors who have the personal knowledge of (person name) Birth.

My birth was registered later because it was not prevalent at that time to register the birth of children within a year. Before I came to United State, I did not have my driver license from Nepal. As for religious document, there is no such thing as baptismal or other notable religious events in Hindu culture that would help me to produce "religious certificates".

Thank you in advance for your assistance in this matter.


Sincerely,

(your name)

Okay, this is what I gave to USCIS during my 485 filings. My Dad made this from the local ward office and this was on Kathmandu Metropolitan City office letter pad with city rubber stamp and ward admin name and signature.
Note that I went through the new interview process and my interviewing officer read it and was okay with it.

To Whom it may concern

Sub: Birth Certificate

This is to Certify that Mr. (Your Full Name), Son of (Father and Mom Full Name), permanent resident of Kathmandu ward # was born on (Full Date of Birth) Kathmandu Nepal.

Admin name
Title,
and signature.

Thank you everyone for sharing your story.

People at my vdc office are saying, they cannot issue birth certificate now as it is too late. But they can give letter saying I was born there including my parents name. With this document what else I need.
Once again thank you for your help.

That's not true, they should give u certificate (in fact I had the same issue, I registered my birth at 29). Your mom/dad needs to go to the office and it will be done.

My dad went there and they are saying they can't give me birth certificate as they started keeping records way after I was born. I even send sample of my friend's birth certificate who got certificate from different place but they say no. So at this point I will not be able to get birth certificate. Any thing they can give me is letter. Any one had same case where they send other documents except birth certificate to uscis.

Khai K bro, i just made the Birth Certificate from the Ward office, it was not that hard.. They already had the sample, my dad provided the new non expired passport and they made it just referring to the passport with the passport number on it and with my parents name on it. I am not sure why they cannot provide it for your case.

My format for the reference was the same one user provided above:

To Whom it may concern

Sub: Birth Certificate

This is to Certify that Mr. (Your Full Name), Son of (Father and Mom Full Name), permanent resident of Kathmandu ward # was born on (Full Date of Birth) Kathmandu Nepal as per passport number ....... .

Admin name
Title,
and signature.