1. A Hex Editor software such as HxD, Hex Workshop, or whatever you want.
2. A calculator software, the one you have in Windows or any of them that can convert between decimal and hex.

1. First, you have to decide what size of the game window you'd like to make the game run, for the example I'll make the game run in 1500x1000.
2. Go to your calculator software. If you use the one comes with Windows, you'll have to change it to "Programmer" mode. Input "1500" and then convert it to hex format, you'll get "5DC". Next, clear the number and return to Decimal mode, input "1000" and convert it to hex, you'll get "3E8"
3. Go to your Steam userdata folder and browse to \Steam\userdata\{your Steam ID}\382900\local\
4. You'll see a file called "settings.bin". Make a backup and open the file in your hex editor software.
5. The size of the game window stored at the very first bytes there. Window width is at 00000000 and 00000001. Window height is at 00000004 and 00000005.
6. If you want the same window size as my example (1500x1000), change these value to "DC 05" and "E8 03", as we calculated these Hex values from Step #2.
7. Save the file and quit your Hex editor.
8. Run the game and enjoy it.

My example (1500x1000) already removed the black borders but if you want other window sizes and don't want the black borders you'll have to calculate it yourself to find the real size of the game display. The game's aspect ratio is 3:2. For the example: 720x480, 1080x720, 1350x900, 1440x960, and 1620x1080.

Here are some values I calculate for you:

1080x720
38 04 and D0 02

1152x768
00 03 and 80 04

1200x800
B0 04 and 20 03

1350x900
46 05 and 84 03

1440x960
A0 05 and C0 03

1500x1000
DC 05 and E8 03

1620x1080
54 06 and 38 04