Unfortunately , Perdo does not allow you to improve things in this manner.
It can only make something a worse example of what it is.
(page 78 )
I wonder about a Muto effect that affected only the pure glass, not the impurities, and turned it temporarily to water. One could then filter out the 'water' leaving the contaminants aside and let the spell (lets say diameter duration) expire.
That would make clear glass via a fairly simple magical method. Then you shape it with craft magics, add impurities for color, what have you. Just don't drink the 'water'...
This pretty much sounds like the magus in question would need a very good understanding of the process involved in making glass... Which sounds like a rare magus indeed... (Maybe he was an apprentice glassmaker before he was found? ) Or maybe this is the works of the Mysterious Glassmaker cult in Venice?
I do not see it as needing any knowledge of making glass. The only knowedge you need beyond that required for Hermetic Magic is that glass exists as a thing, and that normaly manufactured glass is full of impurities that hinder its clarity, etc. IMHO it is a logical process based on clear-cut critical thinking:
- You decide you want absolutely pure glass - you now have an objective.
- Glass is a substance, mixed with impurities - the may or may not be established, but is implied by many above to be in setting.
- You use a spell to affect glass, nothing else. You are electing not to affect any impurities by logical exclusion (A is not B. Thus target A in order to affect A. You will not affect B by default).
- The spell turns only the 100% pure substance of glass into water.
- You filter the 'water' ... I imagine filtering water with a filter paper or cloth filter of some variety is something any basic Hermetic lab setup will allow. Until the spell duration expires it is water, thus there is no longer any question of how glass behaves, what it is, etc, etc, etc.
- An additional spell may need to applied for perfect 'filtering' but that is achievable in many ways via Hermetic Magic.
I this method as one way a Magus could do it. It has the merit of not trying to be complicated and use all sorts of mundane processes. It uses simple, direct, Hermetic magic.
With this process the question becomes: What is 100% pure glass?
I can see strong arguments both for and against it still having the green bottle-glass color of most period glass. It would, however, be free of any impurities and particulate that normaly blocks light coming through. Thus there is a strong case for it being 'clear' but perhaps dark green (not what we think of as window glass, but maybe 'clear' winebottle glass). All fo those arguments are not relevant to the process above, which produces 'pure' glass ... whatever that might be in the setting.
Nice! I like the glass to water + filtering process. Hopwever, we are moving out of the basic question: you are using a Muto spell here, not rego anymore. So if we follow that logic we simply confirm that Rego magic cannot create pure glass: you need alternative magics here 
Cheers,
Xavi
Ahh yes. Sorry. I guess you want Rego only.
I can't see why Rego couldn't just teleport out the impurities and leave the matrix - just glass. Afterall, the filtering process is only a round about way of not moving little bits of contamination ... this effect might be pretty high level though.
I'd say the reason is that, as an historical person ignorant of exactly what those impurities are, it would be extremely hard to identify, isolate and "Rego" them out, just as it would not be possible to "Rego" a poison or infection from a wound instead of using Creo, or to Rego just maple syrup from a maple tree- that's not exactly how the Technique works, typically.
Also, it would require knowing what those impurities are, and isolating them on a very fine, almost molecular level- certainly possible with magic, but also possibly pushing the Medieval Paradigm.
Making glass is, indeed, "alchemical", just as making gunpowder would be. (The fact that making bread is far more complex, yet not considered alchemy is... another discussion.)
The "natural" blue/green color of glass was remedied (in the 1400's) by the addition of additional chemicals, another "alchemical" process. That makes glass "colorless", but not "optically clear", which is a different problem. If making "clear" glass is similar to this, by addressing the original "sand" with chemicals or processes to remove the impurities, then it certainly would be "alchemical" in nature.
But if it's a matter of merely skimming the impurities off the molten glass, or letting them settle to the bottom, that is no more an alchemical process than skimming the fat off of soup, or melting candle-stubs and letting the wick-ends settle out, and tossing that part of the glass away, and repeating the process until the desired purity is achieved. But until glass was colorless, this purity was not as aggressively pursued, as it was simply not a huge advantage.
(As a side comment, it's interesting to note that many medieval "centers" of glass manufacture were moved as the local forests were depleted to run the kilns. So, one advantage magi would have, or any Glassmaker who accepts service for such, is an infinite supply of high, perfectly controllable temperatures.)
If you consider this from the medival persons viewpoint, anyone can make bread, but making glass is far from a simple thing. Most of the glassmaking ways presented here works from our knowledge of how glass is really made - which is about as relevant as our knowledge of how gunpowder is made. These things are simpler in a world without the Mythic element...