I recently had this situation here in Indiana. Mind you I live in a small rural town and the government officials were very helpful. My bike was a true barn find and had not been registered since 1986.
First stop was to call the local sheriff dept and had a deputy come run the vin to declare it not stolen. He provided me with a printed vehicle inspection form stating a clean status.
Second stop was DMV. There they provided me with a checklist and information on obtaining an Affidavit Of Ownership from the court.
Third stop was to the county clerk office. Showed them the paperwork from BMV and they scheduled me a hearing in small claims court. Essentially what you are doing is providing documentation and convince the judge to declare you the owner of the vehicle and order the BMV to issue a new title.
Fourth Stop was the actual court hearing. It lasted all of 10 minutes in the small claims court. The court then mailed me the order declaring me owner.
Fifth stop I sent the un-opened sealed document to the Indiana BMV headquarters with a small fee and they issued me a new, clean title in my name.
Total cost of this was just over $100. $95 was the court fee, and about $15 for the state BMV title application fee. I tried this route before I went through a title service. They wanted almost $300 for their service, which you essentially sell the bike to them, and then they sell it back to you with a new title. Can't remember the Title Service company name but they were based in TN and I had heard about them here on the forum somewhere.
**edit, found the title service. Please note that I have not used them before, but have read good reviews of their services.
https://www.saintsengine.com/services/title-service/