These files fall into four groups:

/lib/modules/4.13.0-16-generic/kernel/drivers/hid/hid-microsoft.ko /usr/src/linux-headers-4.13.0-16-generic/include/config/hid/microsoft.h

These are drivers and support files for Microsoft-branded input devices (keyboards and mice). They are vaguely Microsoft-related, but probably contain no Microsoft code. You can probably remove them safely, though if you've got Microsoft hardware, you might lose things like support for media keys or extra mouse buttons. I don't think any Microsoft hardware is completely incompatible with the generic USB or PS/2 drivers.

/usr/lib/os-probes/mounted/20microsoft /usr/lib/os-probes/mounted/efi/20microsoft

These are part of the Grub bootloader, used to detect if there is a Microsoft operating system present or not on a separate partition/volume. I'm not familiar enough with the internals of Grub to say if deleting them would be harmless, or if it would break your system entirely.

/usr/share/X11/locale/microsoft-cp1251 /usr/share/X11/locale/microsoft-cp1255 /usr/share/X11/locale/microsoft-cp1256 /usr/share/X11/locale/microsoft-cp1251/Compose /usr/share/X11/locale/microsoft-cp1251/XI18N_OBJS /usr/share/X11/locale/microsoft-cp1251/XLC_LOCALE /usr/share/X11/locale/microsoft-cp1255/Compose /usr/share/X11/locale/microsoft-cp1255/XI18N_OBJS /usr/share/X11/locale/microsoft-cp1255/XLC_LOCALE /usr/share/X11/locale/microsoft-cp1256/Compose /usr/share/X11/locale/microsoft-cp1256/XI18N_OBJS /usr/share/X11/locale/microsoft-cp1256/XLC_LOCALE /usr/share/X11/xkb/geometry/microsoft /usr/share/doc/libx11-dev/i18n/compose/microsoft-cp1251.html /usr/share/doc/libx11-dev/i18n/compose/microsoft-cp1255.html /usr/share/doc/libx11-dev/i18n/compose/microsoft-cp1256.html /usr/share/fonts/X11/encodings/microsoft-cp1250.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1251.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1252.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1253.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1254.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1255.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1256.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1257.enc.gz /usr/share/fonts/X11/encodings/microsoft-cp1258.enc.gz /usr/share/fonts/X11/encodings/microsoft-win3.1.enc.gz

These are files describing the Windows cp125* family of character encodings. You don't want to remove them: things will break badly if you ever visit a website using one of these encodings (about 5% of the web) or try to open a text document using one of them. They're Microsoft-related only in the sense that they describe Microsoft practices.

/usr/share/mime/image/vnd.microsoft.icon.xml