Okay, gven you have a '97 ST1100 and are talking a three piston caliper, it is an ABS2 bike.... the two outer pistons are operated by the SMC on the front left fork by the left front caliper moving when either the front or rear brake is applied.
The two centre pistons on the front calipers are operated by the rear pedal, but require a reasonable push on the pedal to make them work due to other components in the system.
The left front caliper, when the wheel is rotating, then moves upwards activating the Secondary Master Cylinder (SMC) which operates the two OUTER pistons on the rear caliper.
The rear brake pedal only operates the centre piston on the rear caliper AND the two front caliper centre pistons.
The front brake lever only operates the two outer pistons on both front calipers and when the front wheel is rotating, will operate the two outer pistons on the rear caliper....
No amount of front brake lever pulling will move the rear brake outer pistons if the bike is standing still and the front wheel is not rotating.
With the rear caliper removed from the mounting, to remove the pistons to clean them, the centre can be removed by pushing the rear brake pedal gently until the centre piston is far enough out to carefully pull it out of the cylinder... do this over a basin or deep tray with rags covering any paintwork to protect it from the brake fluid that is going to come out of the caliper.
To remove the outer pistons, have someone hold the caliper over the aforementioned tray/basin and then gently grasp the left front caliper an move it upwards to activate the SMC, have the person holding the caliper watch the pistons to tell you when to stop.... before they fall out.... same as before gently pull the pistons one at a time from the caliper.
Once cleaned, the caliper and pistons can be re-assembled with new seals if required positioned in the grooves in the caliper, use red rubber grease to coat the seals before refitting the pistons.... push the pistons carefully back in to the caliper.
When cleaning the caliper make sure the seal grooves are properly cleaned out.
You may want to leave the master cylinder top on to prevent all the fluid draining out, or you may wish to remove it and drain all the fluid and clean out the master cylinders.
If doing an ABS bike you need to do both front and rear ends and bleed both brakes properly as well as following the procedure for ABS brake bleeding....
This can be found in the technical section, I believe!
I have only detailed a small part of the whole process, make sure you read and understand the whole process before starting.....