using System.Runtime.InteropServices;

[DllImport("user32.dll")]
private static extern int SetWindowLong(IntPtr hWnd, int nIndex, int dwNewLong);
[DllImport("user32.dll")]
private static extern int GetWindowLong(IntPtr hWnd, int nIndex);
[DllImport("user32.dll")]
public static extern IntPtr FindWindow(string lpszClass, string lpszWindow);
[DllImport("user32.dll")]
public static extern bool SetLayeredWindowAttributes(
    IntPtr hWnd, int crKey, byte bAlpha, int dwFlags);
[DllImport("user32.dll")]
public static extern bool RedrawWindow(IntPtr hWnd, IntPtr lprcUpdate, 
    IntPtr hrgnUpdate, uint flags);

public const int GWL_EXSTYLE = -20;
public const int WS_EX_LAYERED = 0x00080000;
public const int LWA_ALPHA = 0x00000002;
public const int RDW_INVALIDATE = 1;
public const int RDW_ERASE = 4;
public const int RDW_ALLCHILDREN = 0x80;
public const int RDW_FRAME = 0x400;

private void button1_Click(object sender, EventArgs e)
{
    //设置透明
    IntPtr vHandle = FindWindow("Notepad", null);
    SetWindowLong(vHandle, GWL_EXSTYLE,
        GetWindowLong(vHandle, GWL_EXSTYLE) | WS_EX_LAYERED);
    SetLayeredWindowAttributes(vHandle, 0, 255 / 2/*透明度*/, LWA_ALPHA); 
}

private void button2_Click(object sender, EventArgs e)
{
    //恢复
    IntPtr vHandle = FindWindow("Notepad", null);
    SetWindowLong(vHandle, GWL_EXSTYLE,
        GetWindowLong(vHandle, GWL_EXSTYLE) & ~WS_EX_LAYERED);
    RedrawWindow(vHandle, IntPtr.Zero, IntPtr.Zero,
        RDW_ERASE | RDW_INVALIDATE | RDW_FRAME | RDW_ALLCHILDREN);
}

------解决方案--------------------
楼主别忘了把答案贴上来啊，让我们也学习学习，谢谢

------解决方案--------------------
SetLayeredWindowAttributes