The U.S. government has accused Megaupload of facilitating widespread copyright infringement and shut the site down in January. Even so, some Megaupload customers used its services to back up and share files that belonged to them or represented fair use of copyright material.

The EFF will ask the court on Friday to create a process by which these legitimate users can retrieve their files. The nonprofit is representing Kyle Goodwin, an "interested party" in the case against Megauploadand itsfounderKim Dotcom.

Goodwin, a video journalist who covers high school sports, used a Megaupload premium account to store duplicates of his videos. When his hard drive crashed, Goodwin was left with no access to his work product. The hosting company claims it has no access to user data.

So should users of cloud storage services fear that their data, too, could become collateral damage in a case against copyright infringement?

"I think this case raises pretty serious questions about what happens when you store your data in the cloud and for whatever reason the government or the company decides they're not going to store your data anymore," said EFF spokeswoman Rebecca Jeschke.