The fundamental rights of a criminal are no different from those of any other individual. If we accept that these rights are "unalienable", then the concept of "an eye for an eye" can have no place in a discussion about prisons and punishment.
Liberty is simply the ability to choose.
Physical limits on choice are not in themselves an infringement of the right to Liberty, because all choices are limited by nature. Though I am able to choose to fly, I cannot fly! Gravity - and my lack of wings - is around to keep me from realizing that particular choice.
Just because a person is obliged to do something (eg, honour a contract) does not mean that his right to liberty is infringed. And just because a person is kept from doing something else (eg, committing murder) does not mean this, either.
So, is incarceration per se always an infringement of liberty? No.
However, coercion for the sake of coercion is a violation of the fundamental right to Liberty.
(The right to life is discussed at great length in the pages devoted to capital punishment.)
A prisoner deserves the same protection as any other human being.
The right to property is the right to be secure in one's
possessions (ie, body, mind, time, skill, and what one produces
with these or acquires in exchange for these).
When coercion is used to make the criminal pay the state to cover the costs of the trial and housing and restitution, it is not a violation of human rights, any more than the use of force to ensure the respect of contracts is.
When I use the word "dignity", I simply mean that each man is worthy of being treated like a human being. He must not be enslaved, raped, humiliated.
(This is especially important for the people who do the (mis)treating, because each time one treats another human being with less than respect, disrespect becomes easier.)
In most prisons today, the rights to freedom, life, property and dignity are infringed through psychological and physical torture*, murder, forced labour, and humiliation - either by the guards or by other prisoners. And because we know this to be true, we are willing facilitators in the violation of fundamental human rights.
*to torture 1: To punish or coerce by inflicting excruciating pain 2: To cause intense suffering to (Webster's Collegiate Dictionary)
For an action to be torture, physical pain is not necessary. Spiritual, emotional pain are also the fruits of torture.