This sample will populate a few fields on a Certified Document and the save it without breaking the certification.

FillCertifiedForm.java

/*
 * Copyright Datalogics, Inc. 2015
 */

package pdfjt.cookbook.forms;

import java.io.InputStream;
import java.net.URL;
import java.net.URLConnection;
import java.util.HashMap;
import pdfjt.util.SampleFileServices;

import com.adobe.fontengine.font.Font;
import com.adobe.internal.io.ByteReader;
import com.adobe.internal.io.ByteWriter;
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.PDFSaveIncrementalOptions;
import com.adobe.pdfjt.pdf.graphics.font.PDFFont;
import com.adobe.pdfjt.pdf.interactive.forms.PDFFieldList;
import com.adobe.pdfjt.services.ap.AppearanceService;
import com.adobe.pdfjt.services.ap.spi.APContext;
import com.adobe.pdfjt.services.ap.spi.APResources;

/**
 * This sample will populate a few fields on a Certified Document and the save it without breaking the certification. 
 */
public class FillCertifiedForm {

    private static final String inputPDFURL = "http://dev.datalogics.com/cookbook/forms/BlankInputForm_Certified.pdf";
    private static final String outputDir = "cookbook/Forms/output/";

    static public void main(String[] args) throws Exception {
        /*
         * Get the PDF File
         */
        URLConnection connection = new URL(inputPDFURL).openConnection();
        connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11");
        connection.connect();
        InputStream fis = connection.getInputStream();        
        ByteReader byteReader = new InputStreamByteReader(fis);
        PDFDocument pdfDocument = PDFDocument.newInstance(byteReader, PDFOpenOptions.newInstance());
        /*
         * Set the field values
         */
        PDFFieldList fieldList = pdfDocument.getInteractiveForm().getChildren();
        fieldList.getFieldNamed("FirstName").setStringValue("Joel");
        fieldList.getFieldNamed("LastName").setStringValue("Geraci");
        fieldList.getFieldNamed("Address").setStringValue("101 N. Wacker Drive #1800");
        fieldList.getFieldNamed("City").setStringValue("Chicago");
        fieldList.getFieldNamed("Region").setStringValue("IL");
        fieldList.getFieldNamed("PostalCode").setStringValue("60606");
        fieldList.getFieldNamed("Country").setStringValue("United States");
        /*
         * Get the resources necessary to generate the field appearances
         * after we add the data.
         */
        APResources apResources = new APResources(pdfDocument.getCosDocument().getOptions().getFontSet(), pdfDocument.getCosDocument()
                .getOptions().getDocLocale(), new HashMap<Font, PDFFont>());
        APContext apContext = new APContext(apResources, true, null);
        AppearanceService.generateAppearances(pdfDocument, apContext, null);     
        /*
         * Write out the file
         */
        SampleFileServices.createDir(outputDir);    
        String outputFileName = "FilledAndCerfified.pdf";
        ByteWriter outputFile = SampleFileServices.getRAFByteWriter(outputDir + outputFileName);
        pdfDocument.save(outputFile, PDFSaveIncrementalOptions.newInstance());
        System.out.println("Created: " + outputFileName);
    }
}