TransparentWindow.cs

using System;
using System.Collections;
using System.Collections.Generic;
using System.Runtime.InteropServices;
using UnityEngine;

public class TransparentWindow : MonoBehaviour
{
    [DllImport("user32.dll")]
    public static extern int MessageBox(IntPtr hWnd, string text, string caption, uint type);

    [DllImport("user32.dll")]
    private static extern IntPtr GetActiveWindow();


    [DllImport("user32.dll")]
    private static extern int SetWindowLong(IntPtr hWnd, int nIndex, uint dwNewLong);

    private struct MARGINS
    {
        public int cxLeftWidth;
        public int cxRightWidth;
        public int cyTopHeight;
        public int cyBottomHeight;
    }

    [DllImport("Dwmapi.dll")]
    private static extern uint DwmExtendFrameIntoClientArea(IntPtr hHwnd, ref MARGINS margins);

    [DllImport("user32.dll", SetLastError = true)]
    private static extern bool SetWindowPos(IntPtr hWnd, IntPtr hWndInsertAfter, int X, int Y, int cx, int cy, uint uFlags);

    const int GWL_EXSTYLE = -20;

    const uint WS_EX_LAYERED = 0x00080000;
    const uint WS_EX_TRANSPARENT = 0x00000020;

    static readonly IntPtr HWND_TOPMOST = new IntPtr(-1);

    IntPtr hWnd;

    // Start is called before the first frame update
    void Start()
    {

#if !UNITY_EDITOR
        //Uncomment this if you need it, for my case i don't need it.
        //MessageBox(new IntPtr(0), "Hello World!", "Hello Dialog",0);

        hWnd = GetActiveWindow();

        MARGINS margins = new MARGINS { cxLeftWidth = -1};
        DwmExtendFrameIntoClientArea(hWnd, ref margins);
        SetWindowLong(hWnd, GWL_EXSTYLE, WS_EX_LAYERED | WS_EX_TRANSPARENT);
        SetWindowPos(hWnd, HWND_TOPMOST, 0,0,0,0,0);
#endif
        Application.runInBackground = true;
    }

    // Update is called once per frame
    void Update()
    {
//        SetClickThrough(Physics2D.OverlapPoint())
    }
}