Good question, I've worked on the other end, designing the structure for a specific building developed from a prototype set before, but I've never developed the prototype set. Is it for a retail chain?

i've also not had exactly that arrangement, since the prototypes on which i worked were taken through construction docs for the first ones. but...

there's no standard way, no rules, but only a negotiated agreement (as with all architectural fees, really).

i'd charge whatever your normal fee would be for the first one - what it would typically cost for you to pursue a project of this size/scope through schematic design or design development. but you need to retain your rights to all subsequent construction - your contract needs to stipulate that they can't just go building the thing over and over without your knowledge or compensation. you can then negotiate that each subsequent build would be a discounted fee.

when i've done it and it was pursued through cd's, for example, the first build was 100% fee, the next 67%, the next 33%, and then it never went below 20% thereafter - as long as it was the same exact building! if there were significant changes to any one of the later versions, the fee was negotiated back up to take those changes into account.

i've had to do this both ways (what xray is describing, as well as steven's). for the latter - what steven described, we did something similar, although our fee was fixed for each subsequent build at a lower percentage. we did not do any modifications, although we also forbid the owner from doing the same and did not provide any cad drawings for them to use.

for just doing the design concepts, we worked out a flat fee to provide our services, with no additional compensation for how often they'd reproduce it (in the end, their company folded before doing any of them commercially. thankfully, we were paid...)

personally, i think what you should try to negotiate is a fixed fee for the first one, with a low royalty on the back end of each subsequent. be prepared, though: that way forward is really difficult to convince an owner to do, especially if you're not a 'name' providing something they think no one else can. meaning, if they thing what you're providing is the same (qualitative) that they could get from 10 other firms, you're in a weaker position. if you can prove, almost empirically, that your designs will help make their business more money by providing an iconic type 'brand experience' for them, then you're in a better position overall.

X-Ray. Protect yourself. What I would do is think about the process and how they are to utilize your "prototype", knowing that what ever you design and construct might have some flaws or better put, an exploration through a built mock up. I would set an initial fee based on a standardized fee structure. Why I tell you to be smart is for this reason. If you took the time to be the one who was able to utilize your abilities then get paid for your intellectual property. Find out how royalties work, and if they do plan to make 6000 of your prototypes, than each time one is made and sold, you will make a pretty penny based upon the success of your design and prototype. They might argue this fact, but they hired you to design this thing they could not.

This might work and this may not, but people have royalties on some funny stuff such as logos and other things and each time the certified logo is sold the person with a little copyright leverage still benefits. Ask around. Ask anyone. Go to the Library and read a boring book on this, but to your benefit this could help you down the road.