Earlier quoted context omitted.
Are you asking how the government can prove that the money in Silk Road's accounts are the proceeds of illegal activity? They have digital records all over the place to prove that. The magic of Bitcoin and the internet--where all activity is neatly recorded in server logs with timestamps. They can prove that without proving that Ulbricht is the one that engaged in the illegal activity. Indeed, Ulbricht's contention i…
Does a fee collected for helping with illegal transaction is by itself illegaly obtained money? If you are a cab driver and you have a client that you know is riding your cab to perform illegal trade. Does the police have right to seize your fare? Isn't that something court should determine?
For assets to be forfeited the government literally sues the property[1] and is required to show the item is subject to forfeiture. If the asset is eligible for forfeiture the owner can claim that they are innocent[2] and prevent the property from being forfeited.
In this case DPR is not claiming that the wallet is his. Because if he did he'd likely harm the criminal case against himself.
You can read the order here: http://www.justice.gov/usao/nys/pressreleases/January14/Silk...
Note how the government filed suit against "all assets of Silk Road" - not DPR.
This isn't some secret thing that only the government knows about. You can go to http://www.forfeiture.gov right now and read required notices of forfeiture for all sorts of assets.
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[1] This is how we get court cases with fun names like "United States v. $124,700 in U.S. Currency" and "United States v. Forty Barrels and Twenty Kegs of Coca-Cola"