Quick Tip: I found out that Earthquake works on the random eggs doing this. If you don't want to do the eggs one by one, spam Earthquake.

I had cleared the map of all enemies - am not certain if the eggs that pop into Voidling enemies count or not. If you're going for the achievement, get those too just in case. They are red on the minimap and I did not bother including them because you can see them in battles. While on that subject, there is one enemy egg at the very start of the map.

NE Area
43 Eggs (Labeled the map 42 before finding that last one, which is the 43rd in that area and popped my achievement)

NW Area
9 Eggs

Central Area
2 Eggs

Center-West
1 Egg

South East (all in the Ship)
5 Eggs

Southern Branching Path
5 Eggs

Basic Area
Egg 01
Egg 02
Egg 03

Egg 04

Egg 05

Egg 06
Egg 07
Egg 08
Egg 09
Egg 10
Egg 11
Egg 12
Egg 13
Egg 14
Egg 15
Egg 16
Egg 17
Egg 18
Egg 19
Egg 20
Egg 21
Egg 22
Egg 23
Egg 24
Egg 25
Egg 26
Egg 27
Egg 28
Egg 29
Egg 30
Egg 31
Egg 32
Egg 33
Egg 34
Egg 35
Egg 36
Egg 37
Egg 38
Egg 39
Egg 40
Egg 41
Egg 42
Egg 43

Basic Area
Egg 1
Egg 2
Egg 3
Egg 4
Egg 5
Egg 6
Egg 7
Egg 8
Egg 9

Basic Area
Egg 1
Egg 2

Basic Area
Egg 1

Basic Area
Egg 1
Egg 2
Egg 3
Egg 4
Egg 5

Basic Area
Egg 1
Egg 2
Egg 3
Egg 4
Egg 5