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Sorry, I don't have any tips for you as I generally ignore those few remaining specimens. I have been to so many planets that it's simply not feasible to scan all of them. Often I don't even bother scanning anything at all if I deem the planet to be not interesting enough to bother with it. But I'm interested in knowing how others play this game.
There's no reward for finding all the flora or minerals on a planet - just for the fauna - and like Zak says, you'll end up visiting hundreds of planet if you play long enough. It's a question of which will drive you crazier really - spending endless hours trying to find everything, or having to deal with the fact that sometimes you're not going to be able to
Oh...and minerals and flora are just there. There are no hidden triggers or anything you have to hit to make them appear and no additions to the multi-tool scanner that do anything more than extend its range and/or give you more units for scanning them.
There have been many... many posts about tip/tricks for finding fauna... I'll leave it at just play the game and you'll find them all.
Flora and Minerals - I could give a Gek-ass about... EXCEPT for this guy:
https://steamcommunity.com/sharedfiles/filedetails/?id=2997257221
Oh and regarding Flora - many times there are duplicates... case in point on more than one planet I've named TWO of those "Jed" flytraps and they were listed separately on the discoveries tab.
EDIT: I just 100% this planet for ZERO nanites
https://imgur.com/a/KkPq2QZ
For those rare underground fauna: Check near points of interest. They often have caves near them because the terrain is flattened when they are generated. So, sometimes the game "sees" the flat area of a point of interest as "underground," so that last rare underground critter might just be wandering around above-ground near a point of interest. Also, if you're in a cave, scan upwards for red dots. Because sometimes, critters spawned within a cave will teleport to the surface. Why? I don't know. They just do.
For plants: Look for duplicate plants. There are sometimes two hazardous plants that look exactly alike. I've noticed it with the venus-fly-trap ones and with the gas-spewing ones. Haven't noticed it with the whippy ones, though it's also possible there are duplicates of those. There are also two types of cave marrow plants in caves. I've also noticed duplicate plants on both toxic and desert planets. Specifically on toxic planets, there are "plants" that look more like mineral nodes. There's a type that spawns singly and types that spawn in multiple nodes from the same "root." Those are also different species. On desert worlds, there are barrel-type cacti that also spawn in singles or in clusters which are different species. There are also saguaro-type ones that look very similar but are different species. Same is true for the sodium and oxygen plants on every planet. There's the kind that only spawn singly or in small groups, and then there's the kind that spawn in large patches. They are different species, although they look alike. Other than that, it's just a matter of having a good look around every once in a while while exploring. If you rush through, you'll miss stuff. Like with minerals, some plants are small and spawn in among patches of other larger plants and/or un-scannable undergrowth.
For minerals: They're the most difficult to find them all, unfortunately, and I don't have much in the way of special advice. It's just a matter of stopping and looking at everything fairly frequently. The only bit of advice I have is that there are minerals that spawn only in caves and minerals that spawn only underwater, but I imagine you're probably already aware of that.
Lastly: There is, unfortunately a bug somewhere in the mechanism that keeps count of what you've found. You'll see that when you have the "Exploration" mission active, it'll sometimes say that you've found, say, 17/0 plants. Which means you've no idea how many more there are. It never happens with the animals, only with plants and minerals. I've taken to immediately noting on my spreadsheet how many plants and minerals there are on the planet when I land on it, so if the bug happens, I'll still know where I'm at.
To add on here:
Minerals can also look exactly the same and have slightly different names. There are specific landscape types (bleak rock strewn areas for examples) where minerals and even hazardous plants look the same but are considered a new discovery.
Some critters can have spawn rules that make them extremely hard to locate. Only HG knows the exact rules but some appear to only come out for an hour at very specific times of day- maybe once in 24 hours. Being in the right place at the right time ends up being more luck than skill.
I would recommend not trying what you want to do. Part of game is making those hard decisions about sticking around to search or moving on to a new planet. To the extent I have been persistent, it helps to come up with your own system of leaving a marker behind, moving on, and coming back when you feel fresh for the fight again.
An easy one would be to plop a base computer- that is all you need to teleport back. Keep a written log offline might be another if you really are intent on finishing every planet you explore.
One fly in the ointment: After a period of time your "discoveries" will disappear from your discovery listing. (You retain first discovery rights and that is recorded to server- but the details go away in your menu and the items can be re-discovered by you or someone else)
If you are relying on the game guide for 100% success, be aware you can end up with more than 100% of the counts because of this "feature".
The next option is the reliefs of the terrain, you fly over the planet, if you find valleys with caves (underground also refers to the difference in height of the terrain), you can find it.
If your multitool has a scanner range between 600 and 800 or higher, pressing "C" on the PC or its equivalent on consoles can find the checkpoints, where you also find wildlife.
To finish after the last Singularity update, flying at the height of the clouds, your ship will detect unknown buildings that are also candidates to have rare and underground fauna. You can also press "C" on the PC, with the "Alt" key change the view to see if the ship has found something.
I used to try to discover everything, then I noticed my scan data was gone from a planet I hadn't been to for a week or so. So now, I scan while I am there, when i get bored I move on. Unless, it is early in game and I need the nanites, then I search for a couple of hours before calling the planet quits.
Good hard foot work and using the eyes is ok by me
Often with those types of quests, they have to be done on a specific planet. It'll say to look on the Galaxy Map and go to the marked system. So, if you go to the right planet in the right system, you're guaranteed to find whatever it is that you need.
(Also, there are animals on all planets except for dead ones. And there's only one animal on any Exotic-type planet. But other than on those types of planets, you should have no trouble finding many animals. They'll spawn all around you.)