NVM this, I found the answer:
wixProject.ResolveWildCards(ignoreEmptyDirectories: true)
.FindFile((f) => f.Name.EndsWith("MyApp.exe"))
.First()
.Shortcuts = new[] {
new FileShortcut("MyApp", @"%ProgramMenu%\MyCompany\MyApp") { IconFile = wixProject.ControlPanelInfo.ProductIcon },
new FileShortcut("MyApp", "%Desktop%") { IconFile = wixProject.ControlPanelInfo.ProductIcon }
};