I have a 01 civic manual transmission. Recently the transmission will only go in neutral or 3rd gear. Can't get it into any other gear. Can anybody help me with some insight as to the possible issue?

 

I'd first check the shift cables.
There are two main spots, either in the car, or under the hood.
There are two independent cables, one for a left and right motion, and one for forward and back.
To check the ones under the hood you will have to remove the air intake resonator - the really big plastic box close to the battery.
Take a look at the shift linkage as pictured (disregard the text that tells you to remove things - you do NOT need to do that) and see if anything looks fishy. It would help to have someone get in the car and try to shift gears while you look at the linkage on the transmission and see if there are any obvious issues preventing it from changing gear correctly. You should also actually be able to move the shifters on the top of the transmission by hand and select other gears.

 

Was this problem preceded by a mis-shift during your last drive? I had an instance with an ITR gearbox where I tried to grab 6th - lol there is no 6th - and grabbed reverse while I was booking. Loud chonk, horrible noises. Well I got home, parked the car overnight, and the next day I could NOT grab a single gear. What ultimately solved that issue was pushing the car and rolling it and then I could find them all again.

My gf has a Fiat that DID lose the shifter cables, and the consequence was she could not get 5th or reverse. I suppose there are three cables, one for each pair of gears. Well you KNOW when you don't have the cables for a particular gear because the shift is slack. There is no resistance and the shifter will just flop into the position for the gear with virtually no effort.