Silkroad has a government closure notice, so they obviously obtained control over its servers.

Given that, and given that Silkroad didn't use brainwallets for ops money, control over the Bitcoin private keys - and thus, the bitcoins - is trivial.

Edit: Then again, unless we've seen a huge, tens-of-thousands-of-BTC transaction in the last 48 hours, it's possible that the FBI has merely assumed the above without actually taking possession of the bitcoins. In which case, if a bailed Ross Ulbricht has access to a wallet backup...