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The Apache PDFBox library is an open source Java tool for working with PDF documents. This artefact contains examples on how the library can be used.
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/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.pdfbox.examples.pdmodel;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.pdfbox.io.IOUtils;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.PDDocumentNameDictionary;
import org.apache.pdfbox.pdmodel.PDEmbeddedFilesNameTreeNode;
import org.apache.pdfbox.pdmodel.PDPage;
import org.apache.pdfbox.pdmodel.common.PDNameTreeNode;
import org.apache.pdfbox.pdmodel.common.filespecification.PDComplexFileSpecification;
import org.apache.pdfbox.pdmodel.common.filespecification.PDEmbeddedFile;
import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotationFileAttachment;

/**
 * This is an example on how to extract all embedded files from a PDF document.
 *
 */
public final class ExtractEmbeddedFiles
{
    private ExtractEmbeddedFiles()
    {
    }

    /**
     * This is the main method.
     *
     * @param args The command line arguments.
     *
     * @throws IOException If there is an error parsing the document.
     */
    public static void main( String[] args ) throws IOException
    {
        if( args.length != 1 )
        {
            usage();
            System.exit(1);
        }
        else
        {
            PDDocument document = null;
            try
            {
                File pdfFile = new File(args[0]);
                String filePath = pdfFile.getParent() + System.getProperty("file.separator");
                document = PDDocument.load(pdfFile );
                PDDocumentNameDictionary namesDictionary = 
                        new PDDocumentNameDictionary( document.getDocumentCatalog() );
                PDEmbeddedFilesNameTreeNode efTree = namesDictionary.getEmbeddedFiles();
                if (efTree != null)
                {
                    Map names = efTree.getNames();
                    if (names != null)
                    {
                        extractFiles(names, filePath);
                    }
                    else
                    {
                        List> kids = efTree.getKids();
                        for (PDNameTreeNode node : kids)
                        {
                            names = node.getNames();
                            extractFiles(names, filePath);
                        }
                    }
                }
                
                // extract files from annotations
                for (PDPage page : document.getPages())
                {
                    for (PDAnnotation annotation : page.getAnnotations())
                    {
                        if (annotation instanceof PDAnnotationFileAttachment)
                        {
                            PDAnnotationFileAttachment annotationFileAttachment = (PDAnnotationFileAttachment) annotation;
                            PDComplexFileSpecification fileSpec = (PDComplexFileSpecification) annotationFileAttachment.getFile();
                            PDEmbeddedFile embeddedFile = getEmbeddedFile(fileSpec);
                            extractFile(filePath, fileSpec.getFilename(), embeddedFile);
                        }
                    }
                }
                
            }
            finally
            {
                if( document != null )
                {
                    document.close();
                }
            }
        }
    }

    private static void extractFiles(Map names, String filePath) 
            throws IOException
    {
        for (Entry entry : names.entrySet())
        {
            String filename = entry.getKey();
            PDComplexFileSpecification fileSpec = entry.getValue();
            PDEmbeddedFile embeddedFile = getEmbeddedFile(fileSpec);
            extractFile(filePath, filename, embeddedFile);
        }
    }

    private static void extractFile(String filePath, String filename, PDEmbeddedFile embeddedFile)
            throws IOException
    {
        String embeddedFilename = filePath + filename;
        File file = new File(filePath + filename);
        System.out.println("Writing " + embeddedFilename);
        FileOutputStream fos = null;
        try
        {
            fos = new FileOutputStream(file);
            fos.write(embeddedFile.toByteArray());
        }
        finally
        {
            IOUtils.closeQuietly(fos);
        }
    }
    
    private static PDEmbeddedFile getEmbeddedFile(PDComplexFileSpecification fileSpec )
    {
        // search for the first available alternative of the embedded file
        PDEmbeddedFile embeddedFile = null;
        if (fileSpec != null)
        {
            embeddedFile = fileSpec.getEmbeddedFileUnicode(); 
            if (embeddedFile == null)
            {
                embeddedFile = fileSpec.getEmbeddedFileDos();
            }
            if (embeddedFile == null)
            {
                embeddedFile = fileSpec.getEmbeddedFileMac();
            }
            if (embeddedFile == null)
            {
                embeddedFile = fileSpec.getEmbeddedFileUnix();
            }
            if (embeddedFile == null)
            {
                embeddedFile = fileSpec.getEmbeddedFile();
            }
        }
        return embeddedFile;
    }
    
    /**
     * This will print the usage for this program.
     */
    private static void usage()
    {
        System.err.println( "Usage: java " + ExtractEmbeddedFiles.class.getName() + " " );
    }
}