mortar on MDF – What would you do?

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I moved into my flat last year and I have just removed the existing carpet from the bathroom floor. It looks like the flat originally had tiles on top of MDF. There are now bits of mortar (or whatever the tiles were glued to the floor with) in most places. In some areas it looks like someone tried to remove the mortar and damaged the MDF in the process, leaving dents in the MDF. In other places, the MDF is clean and undamaged. As a result, the floor is now very uneven (and I can see why the previous owner used carpet to cover it up).

I would like to lay anything but carpet – ideally something I can do myself without removing the bathroom suite. Should I try to remove the remaining mortar and fill the dents in the MDF or just try to level the floor with some self-levelling compound? What would you do?

(The flat has concrete floors under the MDF.)
 

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I can't really be 100% certain from the photographs, but I very much doubt that the sub-floor is MDF, chipboard or OSB maybe, but not MDF. That actually looks more like the remains of tile adhesive which was spread onto the top of a fibre underlay board. The actual concrete sub floor is probably beneath that.
 
Are you saying that what can be seen under the tile adhesive is the fibre underlay board? How would you go about prepping the floor for a new surface?

Edit: I have just removed the threshold to the carpeted floor in the next room and the same boards continue seemlessly under the carpet.
 
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I'd probably start by cutting a small 30 x 30mm square out with a multitool to see exactly what it is I'm dealing with (such a small piece can be infilled later). Without knowing that I can't see how you'd proceed

For tiles or a vinyl floor it may be possible to skim the entire floor with an SLC, but I really don't know which product you'd need to use. My own approach for a relatively small room might be to lift the lot and just replace it, but that may depend on whether or not the vanity unit, etc are sat on top of it
 
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The vanity unit, toilet and shower have all been put on top of the boards, so I really don't want to rip them out. I've just tried to remove some of the tile adhesive with a chisel and it comes off more easily than I thought. I'm now thinking I might do that with the whole floor. Then I just need to find a way to smooth out the dips in the board.
 
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