I am changing the cv boot on the car I have got isuzu trooper 03

It can damage the parts that keep the tires on our car if you don't get the CV axles replaced. You should take your car to a mechanic to replace the axles.

if you are trying to reassemble the cv joint ( why ever you would need to pull it apart in the first place as the new boot slips over the assembly)
do it outside of the transmission or you will damage the transmission internals
place the transmission end on a block of wood
line up the shaft and hit the top end with a heavy mallet
( sledge hammer will burr the ends )
of you are just putting the shaft back in the transmission to reassemble the front end , line up the splines and use the mallet to start the splines into place by compressing the circlip

The easy way is to take the inner boot off and take the joint apart. Take new cv axle apart at inner joint and attach to the old one sticking out of axle housing. You will need to get new boot clamp.

unbolt the tie rod end and the lower a arm and it should slide out of there

Under the rubber boot inside the CV joint is a big spring clip round the edge , take this out and then the shaft pulls away from the axle with the CV on it .If you are fitting a new boot cut the old off if not just get the clips off and pull the boot back.

Did you take the shaft out from the wheel hub end too ?

First their are two different front axles in 1996 troopers. Isuzu changed the 4wd system from auto lock hubs to drive control axle.auto lock hube are on the older trooper's with the light and wiper switches on the dash. The same way to change both. Auto hub remove the six hex. screws slide off the hub remove the sirclip from the driveshaft. Newer hub has 6 alan-head screw's again remove them then the hubcap then the sirclip on the shaft and slide off the round spacer. Next 4 bolts from the lower balljoint and the brake's. Pull out the hub until it clear's the shaft remove the inner boot clips slide the inner boot out the shaft. Clean the grease from the end of the axle then with your fingernail feel along any of the 3 tracks in the axle and near the outer end of the track you will find a wirelike split ring slide a screwdriver under the ring and lever it off . Pull out the drive clean off the grease. You will see a sirclip on the end of the joint remove it and slide off the joint. You can replace either boot from that end. The outer joint is held on with a snap ring on the shaft inside the joint and is not easily removed need a hammer and drift to drive off the end and when removed its hard to get the snap ring on the shaft back into its place.You can change both boots from this end as well. Cheers

Go to my profile I have just explained how to change a cv boot on a Trooper. The axle needs to be taken out to change the boot so the same solution. What you call an axle I have refered to as a drive (short for driveshaft) It takes a lot of explaining so save me a lot of writing if you read the solution I gave for changing the CV boot. Cheer's

must remove clips from inside front axle housing!! If the cv joint aint broke DONT FIX IT the boots can be replaced in less than 1 hour with hand tools and the boot is around 20$ at any parts store

Link below may be of some help? When you get there, pick one closest to yours.

http://www.autozone.com/N,315475/initialAction,repairGuide/shopping/repairGuideVehicleSelect3.htm

www.autozone.com might