Perhaps resetting loop counters will do the trick?
Warning: untested!  New lines shown without ">" symbol ...

> [ snip ]
>
> #while (XPos < 100)
>   #while (ZPos < 100 )
>     #declare CityArray[XPos][ZPos]=RNum;
>     #while (FCount <= CityArray[XPos][ZPos])
>       object{Floor translate <0,FCount*8,0>}
>       #declare FCount = FCount + 1;
>     #end//while fcount
>     #declare ZPos = ZPos + 10;

       #declare FCount = 0;    // reset inner loop counter.

>   #end//while zpos
>   #declare XPos = XPos + 10;

     #declare ZPos = 0;    // reset middle loop counter.

> #end//while xpos

Does that help?   rc

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