They were only able to steal 26,000 bitcoins from the silk road merchants and clients and than find and uncover one of his wallets holding 144,000 Bitcoins.
This was done with a multiple year investigation from the FBI and most likely other departments like the NSA to track down him , the server, and his passwords.

These funds were taken under a form of theft called "asset forfeiture" and than they used Parallel construction to lie to the court to cover up their illegal methods of finding and stealing these assets.


Unfortunately, that is not how it works. If you win the trial you have the opportunity to try and prove the bitcoins were yours and legally obtained through an expensive and long court battle. Under asset forfeiture you are guilty until proven innocent and the state literally sues the inanimate objects themselves(I know it sounds like a joke but sadly isn't) This is the reason you must try and secure your bitcoins better with multisig paper wallets. Whether it is a hacker or a bunch of psychopaths in uniform your funds can be stolen with enough effort and a 0 day exploit placed on your computer..