Usually the factory pattern encapsulates the complexity behind creating single object from some sort of "materials", like specification. For example, given a URL, create a connection to the server defined by a URL.
In your case, the canonical Factory pattern would take some specification for the file store (URL, context object, etc.) and create a single file server object. While there's nothing forbidding you from returning a list of objects from a factory method given a list of specifications, it's almost as easy and arguably cleaner to iterate over the list of specs and call the factory method for each one. Something like this:
List<FileServer> fsList = new ArrayList<FileServer>();
for(FSSpec spec : fileServerSpecs)
{
FileServer fs = FileServerFactory.create(spec);
fsList.add(fs);
}
// do something with your list of file servers.
This is also more reusable because there are likely situations where you want to create a single file server from a specification without the bother of creating a single-item list with just that specification to pass to your factory method.