As it turned out in comments, the layers in question are what iText indeed calls layers but what actually in PDF lingo is called optional content groups.
There indeed is a utility class for removing such layers in the iText Xtra package (not the extrajars, but itext-xtra.jar): com.itextpdf.text.pdf.ocg.OCGRemover which makes use of the class OCGParser in the same package.
/**
* Class that knows how to remove OCG layers.
*/
public class OCGRemover
{
/**
* Removes layers from a PDF document
* @param reader a PdfReader containing a PDF document
* @param layers a sequence of names of OCG layers
* @throws IOException
*/
public void removeLayers(PdfReader reader, String... layers) throws IOException
[...]
}
After applying that method to a PdfReader you obviously have to save the changes, e.g. by means of a PdfStamper.