I replaced the saddles that came on my Squier Classic Vibe 60s Thinline Telecaster with Wilkinson compensated saddles. Then, I replaced those with Gotoh compensated saddles. Along the way I purchased and returned a Bensonite set of saddles which look very nice, but required modifications to my guitar I did not want to do.
Once the Gotoh saddles were installed, all I had to do was adjust the intonation. This isn’t difficult. I’ve previously done this type of adjustments on Stratocasters and archtop guitars. But I don’t consider it fun. It is time consuming. Here are some suggestions I’ve found, specific to the Telecaster, that should make this process easier.
Tools needed
Screwdriver
The screws that adjust how close the saddles are to the nut require a #2 Phillips head screwdriver. Use a long shaft screwdriver to avoid coming in at an angle or scraping the top of your guitar. I bought a screwdriver with a 6-inch shaft which works perfectly. An alternative would be an offset screwdriver, but a ratcheting offset design won’t fit.


I protected the top of my guitar by taping a piece of plastic from an old placemat to the surface using blue painters tape. Paper or cardboard would work just as well.
Tuner
I’ve owned many different tuners over the years. I currently own clip-on and pedal tuners as well as 4 different apps that run in my iPhone. Some of these options are better than others. Don’t worry if you don’t have a good tuner. If you are young and still have excellent hearing, you could intonate by ear alone. Any tuner you have will be of assistance.
That said, I find some clip-on tuners, such as my Snark tuners, to be annoying for this task. They latch onto a note when the fluctuation in pitch seems to average out, then won’t release the shown pitch until you mute the strings. Some of my apps are like that too.
My favorite tuner for setting the intonation is the Airyware Tuner app on the Apple iPhone App store. It is a strobe tuning app, less expensive and apparently just as good as the Peterson app.

The Pro Tuner on the paid Fender app is a second choice.

Setting the Intonation
The purpose of intonation is to attempt to make the notes all the way up the guitar neck to be in tune with the open strings. The notes played at the 12th fret should be exactly an octave higher than the open string notes. They won’t be. And because the vintage Telecaster saddle design can only adjust pair of strings instead of single strings, it is more than likely you will be making some compromises.
You need to compare the open note for each string to the octave noted on the 12th fret. You will find suggestions from numerous sources to compare the 12th fret harmonic to the fretted note instead of using the open string. I find no difference, often do both, but as a practical matter always check the harmonic because that’s what I’ve been doing for nearly sixty years.
If the fretted note is sharp compared to the open note (or harmonic), then the saddle needs to be moved farther away from the nut. Turn the adjusting screw clockwise to move the saddle farther from the nut.
If the fretted note is flat compared to the open string note, the saddle needs to be moved closer to the nut. Turn the adjusting screw counter-clockwise to shorten the scale length.
This is an iterative process which might take many tries to get fretted and open string notes close enough together to satisfy you. You should retune to pitch after every adjustment. Although not a requirement, adjusting the saddle position might be easier if you detune before the adjustment, then, of course, retune before checking if fretted and open notes match.
It is also a good idea to fret lightly when checking the 12th fret pitch. Tall frets and a heavy hand will change the pitch more than you think.
Because you only have three saddles to adjust, all you can do is adjust one of each pair and then check the other. This is where compromise comes in if the second string is farther off than the first of the pair.
If you change strings, especially to different gauges than you had been using, you should re-adjust the intonation.
Once my intonation is set, I use it as a check on when to change strings. Dirty, corroded, or damaged strings can be diagnosed because the intonation will be off when the 12th fret harmonic is checked against the fretted note on the 12th fret.