String[] files = new String[] { "File1.pdf", "File2.pdf" };
using (PdfDocument doc = new PdfDocument())
{
    for (int i = 0; i < files.Length; i++)
    {
        doc.Collection.AddFile(files[i]);
    }
    doc.SaveToFile("output.pdf", FileFormat.PDF);
    doc.Dispose();
}	
//Create sub folder and add file into itstring[] files = Directory.GetFiles(@"input/");
string inputFile_1 = "input.pdf";
using (PdfDocument doc = new PdfDocument(inputFile_1))
{
    for (int i = 0; i < files.Length; i++)
    {
        doc.Collection.Folders.AddFile(files[i]);
        PdfFolder folder = doc.Collection.Folders.CreateSubfolder("SubFolder" + i);
        folder.AddFile(files[i]);
    }
    doc.SaveToFile("output.pdf", FileFormat.PDF);
    doc.Dispose();
}