The code below allows you to copy a directory structure with or without sub folders including files. Also includes a callback that can be used to filter out files or folders and reports the copy progress.

/// <summary>
/// Copies a directory structure to the destination.
/// </summary>
/// <param name="source">The directory structure to be copied.</param>
/// <param name="destination">The destination where the directory structure will be copied to.</param>
/// <param name="copySubDirectories">true to copy all subdirectories.</param>
/// <param name="overwriteFiles">true if the destination files can be overwritten; otherwise, false.</param>
/// <param name="callback">Provides a callback function for reporting progress. </param>
/// <remarks><p>The callback invoked just before a file copy occurs providing a way of being notified.</p>
/// <p>The callback parameter order is source file, destination file, progress.</p>
/// <p>If the callback is specified it should return true to allow the file copy to occur.</p> 
/// <p>The progress parameter reports progress from 0 to 100. Values to the left of the decimal represent folder copy progress and values to the
/// right of the decimal from 0.000 to 0.99 represent the current file copy progress for the folder that is being copied.</p>
/// <p>To get the current file copy progress as a value from 0 to 100 use the formula fileProgress = progress - 100 * 100.</p></remarks>
public static void CopyDirectories(string source, string destination, bool copySubDirectories, bool overwriteFiles, Func<string, string, float, bool> callback)
{
    // ensure source folder exists
    if (!Directory.Exists(source))
    {
        throw new DirectoryNotFoundException("The path specified in source is invalid (for example, it is on an unmapped drive).");
    }

    // create destination folder
    Directory.CreateDirectory(destination);

    // get all files in source and copy them to destination folder
    var files = Directory.GetFiles(source);
    var progress = 0f; // used to report the progress from 0 to 100

    // set up action to copy files
    var fileProcessor = new Action<float, string[], string>((folderProgress, filesToCopy, folder) =>
        {
            // copy files
            for (var i = 0; i < filesToCopy.Length; i++)
            {
                // get file
                var file = filesToCopy[i];

                // set default result
                var result = true;

                // build destination filename
                var fileName = Path.GetFileName(file);
                if (fileName == null) // should never happen
                {
                    return;
                }

                fileName = Path.Combine(folder, fileName);

                // check if callback specified
                if (callback != null)
                {
                    // store result from callback
                    result = callback(file, fileName, progress);
                }

                // if result is true we are allowed to copy the file
                if (result)
                {
                    File.Copy(file, fileName, overwriteFiles);
                }

                // (folder progress * 100) + file progress
                progress = folderProgress + ((float)i / filesToCopy.Length);
            }
        });

    // copy initial files
    fileProcessor(0, files, destination);

    // check to copy sub directories
    if (!copySubDirectories)
    {
        return;
    }

    // get the folder tree for the source folder
    var folders = Directory.GetDirectories(source, "*.*", SearchOption.AllDirectories);

    // process each sub folder
    for (var index = 0; index < folders.Length; index++)
    {
        // get folder and increment index
        var folder = folders[index];

        // get files
        files = Directory.GetFiles(folder);

        // crop source root from destination and build destination folder path
        folder = folder.Remove(0, source.Length);
        folder = Path.Combine(destination, folder);

        // create destination folder
        Directory.CreateDirectory(folder);

        // process file copying
        fileProcessor((index / folders.Length) * 100, files, folder);
    }
}