If I would let something mix in the blender and let time go to infinity, will all molecules be separated eventually? Just question out of curiosity. If I would let something mix in the blender and let time go to infinity, will all molecules be separated eventually, i.e. if I open up the blender it will be gas? Or can atoms be separated even? (assuming I'm still strong and ok as time goes to infinity)
 A: There is a definite answer to this, and it's yes, the molecules will eventually separate, but unfortunately this has nothing to do with the blender.
Since we're allowing time to go to infinity, even if we assume that the blender is the only thing that exists in the universe, the molecules (and even the atoms) will break apart due to any of these reasons:


*

*Proton decay, if it occurs on long enough time scales, will change the chemistry of the molecules and cause them to come apart.

*Quantum-tunneling into black holes: on long enough time scales, all matter can quantum-tunnel into a black hole. Since the resulting black hole will be microscopic, it will quickly evaporate as Hawking radiation.

*The heat death of the universe: all matter will eventually ionize, due to the continuing expansion (i.e. decreasing density) of the universe.
And if the blender is not the only thing that exists in the universe, e.g. if the blender is on Earth, then the molecules will break apart for other more practical reasons, for example when the Sun becomes a red giant and disintegrates the Earth.
(It goes without saying that the blender itself will be subject to all of these consequences along with its contents.)
A: The dull and simple answer is no.
Why not? Well the universe tends to go the lowest energy state and highest entropy. Of course should you put enough energy in then you should be able to break molecules apart. However this is the problem, the energy a blender provides is far from enough to break stable molecules apart. The impact on most molecules due to the blender will be low, especially as the particles become smaller and smaller as they will just start to bounce off because of their low mass and how easy it is to change their momentum. 
This is an experiment you can do at a finite timescale though. Grab something (preferrably something you have many off and something cheap), I suggest ping pong balls, and throw it in the blender and start the blender at some point it will seems like it's not making it much smaller (probably 2 minutes or so). Note down the time and repeat but with doubling the time and then repeat once more doubling the previous time. Then get some sieves, and what you'll see is that the smallest particle you get stays probably around the same (the quantity might be different though) By example:
$$
\begin{array}{c|cccc}
\hline
\text{} & \text{Experiment 1} & \text{Experiment 2} & \text{Experiment 3} & \text{Experiment 4} \\
\hline
\text{Time (minutes)} & 2 & 4 & 8 & 16 \\
\text{Smallest sieve size} & \text{No. }\sim 80-100 & \text{No. } 100 & \text{No. } 100 & \text{No. } 100 \\
\text{Amount (grams)} & 1.8 & 3.9 & 4.7 & 5.5 \\
\hline
\end{array}
$$
