No you cannot store folders in Amazon S3.
However, In Amazon S3 buckets and objects are the primary resources. You store objects in the bucket, it is a flat structure with no hierarchy that you see in a typical file system. However, Amazon S3 console supports the folder concept using the object key name prefixes. For example, you can create a folder, photos, in the console and store an object myphoto.jpg in it. But the folder concept is only supported in the console not in Amazon S3. In Amazon S3 the object is stored in the bucket with key name photos/myphoto.jpg. In other words, the console supports the concept of folders using the key names. The following are two more examples:
If you have three objects , logs/date1.txt, logs/date2.txt, and logs/date3.txt in your bucket, the console will show a folder named logs. If you open the folder you will see three objects, date1.txt, date2.txt, and date3.txt.
If you have object name photos/2013/example.jpg, the console will show you folder photos containing folder 2013, containing the object example.jpg.
So the console uses object key names to present folders and hierarchy, in Amazon S3 you only have buckets and objects.