Make a File/Folder Hidden on Windows with Java

For Java 6 and below,

You will need to use a native call, here is one way for windows

Runtime.getRuntime().exec("attrib +H myHiddenFile.java");

You should learn a bit about win32-api or Java Native.

The functionality that you desire is a feature of NIO.2 in the upcoming Java 7.

Here's an article describing how will it be used for what you need: Managing Metadata (File and File Store Attributes). There's an example with DOS File Attributes:

Path file = ...;
try {
    DosFileAttributes attr = Attributes.readDosFileAttributes(file);
    System.out.println("isReadOnly is " + attr.isReadOnly());
    System.out.println("isHidden is " + attr.isHidden());
    System.out.println("isArchive is " + attr.isArchive());
    System.out.println("isSystem is " + attr.isSystem());
} catch (IOException x) {
    System.err.println("DOS file attributes not supported:" + x);
}

Setting attributes can be done using DosFileAttributeView

Considering these facts, I doubt that there's a standard and elegant way to accomplish that in Java 6 or Java 5.