So how do you actually go about opening an apprentice to the arts when he has a a major supernatural virtue? In character creation it is a simple matter but very difficult in game.
The main book says the target number for Lab Total is 60 is you wish to preserve the ability but how do magi go about achieving this number? How do you get a Lab Total so high? Can you use experimentation?
It seems a rather high target to achieve.
IMS there are lab specialists that do the Opening for a price. That lab total is fairly normal for an experienced magus in the field, so it is no biggie for them. As other specialists in the OoH selling their services, there will be 2-4 dudes at any time selling just that kind of service to the wider Hermetic community.
Xavi
Agree with Xavi.
I think it's either a tranorma or a pralician who does this normally - for a fee (+VAT).
Other question, can the opening be made with lab helpers like others lab Activities or works?
I can't see why not. I would assume that the magus that wants the apprentice opened would be acting as a lab assistant anyway 
Xavi
IMS, we made it a team effort and used Leadership. Our InVi specialist who had could cast Sight of the Active Magics had a fairly high lab total, so after a little tuition in Leadership from a friendly noble companion, he was able to use a team to help (Leadership 2, specialisation Magi, allowed him to add 3 peoples Int + Magic theory to the lab total) so we could make a gifted shapeshifter into an apprentice.
We also looked into modifying the lab, but there are very few things that add to Vi and only features & foci and other "general" bonuses add to In, so unless we wanted to add a greater feature of an Orb or Scrying mirror there wasn't much point.
Ok, so the Specialist could be very prized, but could be substitued on houses with one Initiation thinking; just like the Merinita taht have many members with Supernatural Virtues, the faeric. I'd say taht one Vis fee could be very high, having in mind that the Specialista have very high Vim totals, and that is the individual prize by service.
I had an experienced bonisagus (96 years out of apprenticeship) with lab total of
Int 3+Mt 13 (11+2)+aura 7 + Familiar's bonus 10 (int 2+mt 8) + Lab 5 (5 general, other bonuses didn't apply to Vim) for a total of 38 before even adding in arts. This left her only 22 short for the necessary 60. In her focus she could easily get lab totals of 120 or more (19 cr *2, Terram 27, +8 terram/+2 creo lab specialties, MT specialty for her and her familar).
Now her arts were such that I think she was short but could have fixed it in a couple seasons (I forgot what arts are used, it CrVi then she had it, if other technique, she was 3 pts short). Even if she was short, she easily could have gotten a hand for 1 season to do it since who wouldn't want a +16 to lab total helping them for a season in return.
Now admittedly,magic theory that high is a real dedication but it makes sense for a covenant to have a highly specialized vim lab (+8-10 for vim) for use with vis extraction, opening apprentices to the arts and so on that as long as it is not refined, anyone can use it for the benefit. Then you only need level 50 (10 from lab). A 50 total isn't really that hard to get.
I have been working under the assumption that because lineages in House Ex Miscellanea have at least one Major (usually) Supernatural Virtue, that the Initiation rite for Opening the Hermetic Arts of the Apprentice must have been modified account for the lineage Supernatural Virtue, and transmitted down the generations. Otherwise House ex Miscellanea would probably died out and/or become vanilla Hermetic.
This would suggest that once some (ex Miscellanea) mage somewhere sometime works out the trick for including a particular supernatural virtue in Hermetic opening, then that Trick can be taught to another Magus.
Which could give individual members of House ex Miscellanea a rather good bargaining position.
I would guess that for Ex Misc, the exact method for opening arts with a specific supernatural virtue is taught as part of the tradition and is a special rite or like an initiation. It would have been worked out when the tradition was integrated into magic theory (and the minor virtue determined).