You can change the default font in notepad with the following registry keys (this will set to "Courier New" and size of 9):
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Microsoft\Notepad]
"lfEscapement"=dword:00000000
"lfOrientation"=dword:00000000
"lfWeight"=dword:00000190
"lfItalic"=dword:00000000
"lfUnderline"=dword:00000000
"lfStrikeOut"=dword:00000000
"lfCharSet"=dword:000000b2
"lfOutPrecision"=dword:00000003
"lfClipPrecision"=dword:00000002
"lfQuality"=dword:00000001
"lfPitchAndFamily"=dword:00000031
"lfFaceName"="Courier New"
"iPointSize"=dword:0000005a
EDIT :
To change the registry using c# see here :
Read, write and delete from registry with C#[
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