Monster lairs are usually not thought of much in monster design, and for good reasons. Many do not have lairs or use existing structures. But there are some that either create their own or alter an existing one so much that it is effectively new. Here are 5 monsters from the MF core book and what I consider typical lairs for each.
Fungoids already have a lair described, underground near pools of radioactive water. They use the water for their larvae. Okay, but not much to go on, so I considered some ideas and came up with a science experiment that children have done for decades, if not centuries. The waters are not only radioactive, they also react to the waste products of the tiny fungal critters by growing crystals. The longer the habitation, the larger the size of these yellow and purple crystals. Eventually the fungoids are forced to evacuate and seek the water elsewhere. Of course the crystals also displace the water, causing it to leak from the pools. In some cases it is nearby and thus the fungoids don't have to move far; in others it drains into the ground water and causes mutations deep in the soil and potentially many miles away after a few years. The crystals are useful to some android and robot communities as weak power sources that slowly release their energy over decades. The machines look to them for survival rather than advancement of their actions. Considering the number of power cells and power plants that are destroyed in the wastes each year, this is a farsighted strategy.
Kamatas have no listed habitat, much less lair. Considering their lack of hands and apparently poor digging skills, I ended up deciding they are like bower birds and take the lairs of others, be they caves or ruins. The kamatas have a constant electrical charge so they may seek rare metals and exotic matter that make this defense more useful as well as attract mates. Metals simply allow the creature to touch part of their lair and fry creatures in another. The matter could do just about anything, from blind to poison to animate and attack when exposed to the creature's innate charge. Of course the kamata may also be vulnerable to some of these traits.
Mants are intelligent ants with hands. They do have ant like hives but I want to make them different from giant ants and ant horrors. It isn't their mental mutations, but rather their insect ancestry that give them an advantage- sticky silk. They could use it in their hives to create both ways for them to walk on walls and ceilings as well as traps for intruders. The mants are intelligent enough to use technology and artifact enhanced traps are common enough to kill those foolish enough to seek the queen.
Pumpkin men could be the basis of a couple cliches as lairs- pumpkin patches and bone yards from the animals they slay. Eh. I also wanted to avoid the master plant using non-sapient slaves as they do not have mutations that jive with that theme. So I came up with treehouses made of vines. In the case of the typical temperate locations of MF campaigns, I would go with mutant grapevines, but just about any (including pumpkins) can work. Living in trees allow them some sense of security from ground based herbivores and allow them to rain death upon their foes. With a little luck and the right season, they may even use the leaves of the vines or trees as camoflauge.
Vomit flies usually do have lairs oddly (it is in their stat block), but I do not think they would have anything that is typical- just somewhere to rest protected from the elements. What they do have is a cold damage inflicting attack. Their lair will be very chilly and will have cold adapted species living in it. What I ended up with is mutant algae. The slime doesn't have a physical attack, usually, but seems to specialize more in mental mutations. They may end up slaying their hosts and slowly dying from the heat as the lair warms. In any case, they will provide an additional challenge for the PCs who explore the flies' home and see what loot they can find.