The phrase "bottom part" refers to the lower section or piece of something. It is the part that is located at the opposite end from the top or topmost section. Full definition
When it did start to heal, her broken bone set in a side by side alignment instead of the top part of the bone being attached on bottom part of the broken bone. (halifaxveterinaryhospitalinc.com)
Remove bottom part of dough from freezer or fridge. (lapechefraiche.com)
Maybe just paint the very bottom part (the base) white and leave the rest as it is. (theletteredcottage.net)