Here is the steps to get a Nano Cube:
1) Nophex Cube. Drops from mission bosses.
2) Pattern. Drops from unique bosses (see below).
3) Combine Nophex Cube and a pattern and you end up with filled Nophex Cube.
4) Add Kenneth's Polishing Gel to the filled Nophex Cube, and the result will be Nano Cube.
The Complete List:
Code:NT Dot's Pattern Name Drop from Nano Name Lvl req Pattern of Approaching Death (Hezak) => Cellular Re-Structure (AI 17) Pattern of Impending Death (Hezak) => Poisoned Thorns (AI 21) Pattern of Invitable Death (Ghasap) => Frost Blades (AI 25) Pattern of Imminent Death (Ghasap) => Magma Covering (AI 27) Pattern of the Occurence of Death (Bio Dome) => Self Illumination (AI 28) MP Pet Pattern of Indomitable Life (Bio Bome) => Summon The Rihwen (SL 220)