I might get some hate mail for this due to the way I’m providing the information. ^^ The thing is, it’s extremely time-consuming to piece together the map (and it doesn’t help that the map is wider at the bottom so moving the map down or up will mess up the perspective) and I’m way too lazy to manually redraw the bloody thing myself.
Anyway, the following screencaps are from the Japanese version which is identical to the localized one. I did this to help myself get the damnable Stupendous Scavenger trophy since I couldn’t figure out which point I was missing for the life of me. There are so many images due to the fact that the back button, marker button and other shit cover up parts of the map as you move it around.
Take note that there are some harvest points that overlap such as the two mineral points in the dead-end area in the eastern most part of the Forest of Dawn in the second screenshot.
Harvest Points
Please ignore the chests since not all of them are shown!
As for the dungeons, here’s the list of the quantities of materials found in each location:
- Casnan Mine – 2
- Waterfall Cave – 6
- Forest of Dawn: Sunlit Ruins – 6
- Forest Labyrinth – 2
- Ancient Burrow – 11
- Underground Ruins – 6
- Jade Cave – 10
- Misty Peak – 4
- Sacred Beasts’ Lair – 6
- Mt. Vesuvio: Snowy Peak – 15
- Colonia Artifact Laboratory – 6
Chest Locations
There are several Japanese walkthrough sites that do make note of them although I’m not sure how accurate they are. If you’re curious, do a Google search for セルセタの樹海 with the term 宝 (treasure) or 宝箱 (treasure chest) next to it.
Heh. I just did a search myself and came across this blog posts which shows all chests in the dungeons only. It has screenshots to help you locate them! http://huteikigame.blogspot.ca/2012/10/ps-vita_18.html
And there’s this page with the handdrawn world map showing chest locations AND harvest points. However, please be aware that there’s every chance some information might be missing: Great Forest area and The Primeval Lands
koukoupuffs 
Greetings!!
I am glad that I could be of assistance to you.
see you.
Many Thanks for this is really helpful.
See you
hi. how do you get to the small river under the right side of the tree on the map?
Wow. I never even noticed it. ^^ How far are you in the game? I THINK you get it after filling up the area southeast of it and visiting Comodo? Sorry but it’s been too long since I’ve last played it.
Oh! As it turns out, it does kind of fill in early in the game: https://koukoupuffs.net/2012/10/01/ys-celceta-log-4/
Gotta say, thanks for saving my butt, I had 100% map but was missing 1 harvest point. It was killing me, but found it on your pics. Thanks!