This Gist shows how to exclude specific annotation types from being flattened by the FormFlattener.

FlattenEverythingExceptLinks.java

package pdfjt.cookbook.document;
import com.adobe.fontengine.font.Font;
import com.adobe.internal.io.ByteReader;
import com.adobe.internal.io.InputStreamByteReader;
import com.adobe.pdfjt.pdf.document.PDFDocument;
import com.adobe.pdfjt.pdf.document.PDFOpenOptions;
import com.adobe.pdfjt.pdf.document.PDFSaveFullOptions;
import com.adobe.pdfjt.pdf.graphics.font.PDFFont;
import com.adobe.pdfjt.pdf.interactive.annotation.PDFAnnotationEnum;
import com.adobe.pdfjt.services.ap.spi.APContext;
import com.adobe.pdfjt.services.ap.spi.APResources;
import com.adobe.pdfjt.services.formflattener.FormFlattener;
import com.datalogics.pdf.document.DocumentHelper;
import java.io.InputStream;
import java.net.URL;
import java.net.URLConnection;
import java.util.EnumSet;
import java.util.HashMap;

/**
 * This Gist shows how to exclude specific annotation types from being flattened by the FormFlattener.
 */
public class FlattenEverythingExceptLinks {

    private static final String inputPDF_URL = "http://practicalpdf.com/downloads/selectiveFlattening.pdf";
    private static final String userAgent = "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11";

    public static void main(final String... args) throws Exception {
		// First get the PDF file
		URLConnection connection = new URL(inputPDF_URL).openConnection();
        connection.setRequestProperty("User-Agent", userAgent);
        connection.connect();
        InputStream fis = connection.getInputStream();
        ByteReader byteReader = new InputStreamByteReader(fis);
        PDFDocument pdfDocument = PDFDocument.newInstance(byteReader, PDFOpenOptions.newInstance());
        // Create the resources object we'll need for flattening
        APResources apResources = new APResources(pdfDocument.getCosDocument().getOptions().getFontSet(),
                pdfDocument.getCosDocument().getOptions().getDocLocale(), new HashMap<Font, PDFFont>());
        // Create the context we need for limiting the flattener
        APContext apContext = new APContext(apResources, true, null);
        // Add all of the annotation types to the set we are going to flatten
        EnumSet<PDFAnnotationEnum> annotationsToProcess = EnumSet.allOf(PDFAnnotationEnum.class);
        // Remove just the link annotation type
        annotationsToProcess.remove(PDFAnnotationEnum.Link);
        // now set this set of annotation types as the ones to flatten.
        apContext.setAnnotationsToBeProcessed(annotationsToProcess);
        FormFlattener.flattenDocument(apContext, pdfDocument, null);
        // Save and close the file.
        DocumentHelper.saveAndClose(pdfDocument, "selectiveFlattening_Output.pdf", PDFSaveFullOptions.newInstance());
        System.out.println("Done!");
    }    
}