Are you planning to applique with the sewing machine? I strongly recommend a nice cotton thread instead, but if you want a clear one, try looking at your local quilt store for clear polyester thread. It's a good substitute for nylon.
http://softexpressions.com/software/threads/Invisible.php
From their website:
Superior MonoPoly is made of polyester, not nylon. The advantages of polyester monofilament are numerous:
Polyester has a much higher heat resistence than nylon.
Polyester monofilament does not go brittle over time.
Polyester monofilament does not discolor or "yellow" over time.
Polyester is softer and more pliable than nylon, meaning it will lie better on and in the fabric.
How to use:
Use in the sewing machine, bobbin, and serger.
QUILTERS: Used for machine quilting and invisible machine appliqué.
Match the value of your fabric to the clear or smoke thread and it will blend into the fabric for a hand look by machine when doing applique or quilting.
Use in bobbin or on the top when appropiate for decorative sewing methods without the anchoring bobbin thread showing.:
Machine and free-hand embroidery
Machine beadwork
Couching heavy threads
In the serger used for floating decorative edges and floating decorative flatlock.