Following code will create directories (if not exists) & then copy files.
// using System.IO;
// for ex. if you want to copy files from D:\A\ to D:\B\
foreach (var f in Directory.GetFiles(@"D:\A\", "*.*", SearchOption.AllDirectories))
{
var fi = new FileInfo(f);
var di = new DirectoryInfo(fi.DirectoryName);
// you can filter files here
if (fi.Name.Contains("FILTER")
{
if (!Directory.Exists(di.FullName.Replace("A", "B"))
{
Directory.CreateDirectory(di.FullName.Replace("A", "B"));
File.Copy(fi.FullName, fi.FullName.Replace("A", "B"));
}
}
}