ASP.Net Uploadify Plugin save multiple files to Dynamic Folder

You can make use of scriptData parameter of uploadify to pass folder name

<script type="text/javascript">
    $(window).load(
    function () {
        $("#<%=FileUpload1.ClientID %>").fileUpload({
            'uploader': 'scripts/uploader.swf',
            'cancelImg': 'images/cancel.png',
            'scriptData': { 'FolderName': 'NewFolder' },
            'buttonText': 'Browse Files',
            'script': 'Upload.ashx',
            'folder': 'uploads',
            'fileDesc': 'Image Files',
            'fileExt': '*.jpg;*.jpeg;*.gif;*.png',
            'multi': true,
            'auto': true
        });
    }
);
</script>

Then in code fetch the Folder name and use it for saving image

    public void ProcessRequest (HttpContext context) {
        context.Response.ContentType = "text/plain";
        context.Response.Expires = -1;
        try
        {
            HttpPostedFile postedFile = context.Request.Files["Filedata"];
            string folderName = context.Request.QueryString["FolderName"];

            string savepath = "";
            string tempPath = "";
            tempPath = System.Configuration.ConfigurationManager.AppSettings["FolderPath"];
            savepath = context.Server.MapPath(tempPath) + "\\" + folderName;
            string filename = postedFile.FileName;
            if (!Directory.Exists(savepath))
                Directory.CreateDirectory(savepath);

            postedFile.SaveAs(savepath + @"\" + filename);
            context.Response.Write(tempPath + "/" + filename);
            context.Response.StatusCode = 200;
        }
        catch (Exception ex)
        {
            context.Response.Write("Error: " + ex.Message);
        }
    }