In order to uninstall miniconda, simply remove the miniconda folder,

rm -r ~/miniconda/

As for avoiding conflicts between different Python environments, you can use virtual environments. In particular, with Miniconda, the following workflow could be used,

$ wget https://repo.continuum.io/miniconda/Miniconda3-3.7.0-Linux-x86_64.sh -O ~/miniconda.sh
$ bash miniconda
$ conda env remove --yes -n new_env    # remove the environement new_env if it exists (optional)
$ conda create --yes -n new_env pip numpy pandas scipy matplotlib scikit-learn nltk ipython-notebook seaborn python=2
$ activate new_env
$ # pip install modules if needed, run python scripts, etc
  # everything will be installed in the new_env
  # located in ~/miniconda/envs/new_env
$ deactivate

Can I remove the miniconda3 library?

Yes, you can remove the library.

Why miniconda3 is in /opt/ instead of ~/miniconda3/?

I don't know why, but the miniconda3 is in the /opt/miniconda3.

You may uninstall miniconda3 with the following commands:

1. cd /; rm -rf ~/.condarc ~/.conda ~/.continuum
2. cd opt
3. sudo rm -rf miniconda3
4. Open your bash or zsh rc file to remove miniconda from your path variable.

I used zsh, so I open -e ~/.zshrc to delete the context:

# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$(CONDA_REPORT_ERRORS=false '/Users/yilin/opt/anaconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
    \eval "$__conda_setup"
else
    if [ -f "/Users/yilin/opt/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/Users/yilin/opt/anaconda3/etc/profile.d/conda.sh"
        CONDA_CHANGEPS1=false conda activate base
    else
        \export PATH="/Users/yilin/opt/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda init <<<

To uninstall miniconda do the following:

brew uninstall --force miniconda

Additionally, you might have done conda init "$(basename "${SHELL}")" for your respective terminal. To reverse that what I do is write the following: code .bashrc or code .zshrc in my terminal. This will open the respective file in VSCODE and you can delete the chunk of script that activates conda environments in the respective bash or zsh terminal.

Or you can just use the following:

For Bash

conda deactivate
conda config --remove-key "auto_activate_base"
conda init bash --reverse

For zsh

conda deactivate
conda config --remove-key "auto_activate_base"
conda init zsh --reverse

Basically, all it does is delete the (base) in your respective terminal by removing the activation script of conda. So, the reverse of the command conda init "$(basename "${SHELL}")".