I have been cutting some mdf sheets using a jigsaw. I've been marking nice straight pen lines for me to follow, and I can follow these perfectly so that I am getting a nice straight cut on the top face. However, when I turn the cut panel over, I find that the jigsaw blade has not followed the same straight line underneath and I end up with a wavy edge instead of a nice square edge.
I've tried both a small tooth blade and a large wide tooth blade (both for wood) and still have the same problem, although the large tooth blade is slightly better. I've even tried using a table saw on some panels but I find that exactly the same problem occurs. I'm pretty certain that I'm keeping the jigsaw flat to the wood and upright at all times.
My guess is you're achieving the best you can from the tools you're using. With Jigsaws, even expensive ones, the blade tends to wander from the vertical - straight on top, wonky underneath. I'd suggest testing the pendulum action as well as the straight vertical action and see which produces the best result.
The best solution is to use a circular saw/skill saw, possibly with a guide rail or fence and clamps.
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