The accused mastermind of the online black market Silk Road has pleaded not guilty to a host of criminal charges in a New York federal court.

Ross William Ulbricht, 29, wearing a blue prison suit for his arraignment, has denied all charges against him that he created and managed Silk Road.

Authorities claim Ulbricht is the infamous “Dread Pirate Roberts” who operated the underground site, an encrypted network that allegedly sold drugs, weapons, hacker tools and “hit” services to kill people.

US District Judge Katherine Forrest set a trial date of November 3 in the case.

The government arrested Ulbricht in October on a criminal complaint charging him with drug trafficking and related offences.

An indictment unsealed on Tuesday charged Ulbricht with money laundering and conspiracy to commit computer hacking, and with running a criminal enterprise, which carries a minimum sentence of 20 years in prison.

As part of the operation, US authorities seized a large cache of Bitcoins, a virtual currency used in Silk Road transactions.

Prosecutors say they have seized 173,991 Bitcoins, worth over $US150 million ($A168 million) at present exchange rates, in the investigation.

Authorities also filed criminal charges in January against two operators of a Bitcoin exchange, claiming they violated money laundering laws by allowing its users to buy drugs and other illicit goods on the Silk Road website.

Ulbricht was using a laptop in a San Francisco library when he was arrested on October 1 and investigators were expected to scour the machine for evidence he is indeed “Dread Pirate Roberts”.

The online moniker appeared to be taken from a character in the film “The Princess Bride.”